cleveragents-core/CHANGELOG.md

Changelog

All notable changes to this project will be documented in this file. The format follows Keep a Changelog.

[Unreleased]

Added

• TUI — First-run experience with actor selection overlay: On first launch (no personas configured), a centred ActorSelectionOverlay widget guides the user to select an actor from a curated list (anthropic/claude-4-sonnet, anthropic/claude-4-opus, openai/gpt-4o, openai/o3, google/gemini-2). Supports keyboard navigation (j/k), fuzzy search (/), and confirmation (enter). Selecting an actor creates a "default" persona and dismisses the overlay. Subsequent launches restore the last active persona. (#1391)

• TUI — Session export to Markdown transcript: agents session export gains a --format flag accepting json (default, canonical, re-importable) and md (human-readable Markdown transcript via Session.as_export_markdown()). The Markdown format renders a header with session metadata, full message history with role/timestamp/content, and linked plan references. The /session:export [--format md] [path] and /session:import <path> slash commands are also wired in the TUI command router. (#1004)

• ACMS — UKO provenance tracking and temporal versioning: The UKO runtime now records provenance metadata (sourceResource, validFrom, isCurrent) on every typed triple produced by UKOIndexer.index_graph(). A revision chain tracks ontology state across indexing runs, enabling temporal queries over historical UKO snapshots. UKOGraphPersistence serialises/restores the full graph (including provenance) via JSON-file or in-memory backends, satisfying the "persists across restarts" requirement. 47 new BDD scenarios cover typed triples, temporal queries, and provenance. (#891)

Fixed

• agents tool add now accepts YAML configs using the spec-required tool: wrapper key (e.g. tool:\n name: ...). The cleveragents: version header is silently ignored. Flat format (without wrapper) remains supported for backward compatibility. (#1471)

• Session export checksum format corrected from raw hex to sha256:-prefixed format as required by the specification. (#1450)

• ThoughtBlockWidget background corrected from $primary 20% to $primary-muted 20%, making thought blocks visually lighter and more subtle per spec §29811. (#1448)

[3.7.0] — 2026-04-02

Added

• TUI — Interactive Terminal UI (agents tui): Full-screen Textual-based application with multi-session tabs, real-time plan monitoring, and rich conversation with actors. Requires the optional cleveragents[tui] extra. (ADR-044)

• TUI — Persona system: YAML-backed personas stored in ~/.config/cleveragents/personas/. Each persona binds an actor, optional argument presets, and scope references to a named identity. Personas are managed via /persona:* slash commands or the PersonaRegistry API. Per-session state (active persona, active preset) is tracked in memory and the last-used persona is persisted to tui-state.yaml. (ADR-045)

• TUI — Input mode routing: The prompt auto-detects three input modes from the first character — Normal (message + @reference expansion), Command (/ slash commands), and Shell (! subprocess passthrough). The InputModeRouter dispatches each mode to the appropriate handler. (ADR-046)

• TUI — Slash command catalog: 67 slash commands across 14 groups (Session, Persona, Scope, Plan, Project, Actor, Resource, Config, Tool, Skill, Invariant, Profile, Context, Utility) exposed via the SlashCommandOverlay widget and SLASH_COMMAND_SPECS catalog.

• TUI — Context-sensitive help panel (F1): HelpPanelOverlay toggled by F1 with content that adapts to the current prompt context (Main Screen, Slash Commands, Reference Picker, Shell Mode). Global key bindings are always shown alongside context-specific shortcuts. (#1013)

• TUI — Persona bar: Bottom status bar (PersonaBar) displaying the active persona name, bound actor, current argument preset, and scope reference count. Cycle presets with Ctrl+T.

• Session management: agents session command group with create, list, show, delete, export, import, and tell subcommands. Sessions are persisted via the DI-wired SessionService and routed through the A2A local facade. Fixed DI container wiring (session_service provider) that previously caused AttributeError on all session commands. (#554, #570)

• Server mode: agents server connect persists server URL and token to configuration. agents server status reports connection state. Kubernetes Helm chart added in k8s/ for production deployment with Deployment, Service, Ingress (TLS), ConfigMap, ServiceAccount, Secrets, and optional Redis subchart for multi-instance session affinity. Dockerfile.server provides a multi-stage ASGI container image. (#928)

• A2A integration: A2A local facade handlers wired to live application services — session.create/close, plan.create/execute/status/ diff/apply, registry.list_tools/list_resources, event.subscribe. Domain-to-A2A error code mapping (NOT_FOUND, VALIDATION_ERROR, INVALID_STATE, PLAN_ERROR). (#501)

• TUI — PermissionsScreen with diff view: Full-screen overlay for tool permission requests. Displays a file list on the left and a diff view on the right. Supports three diff display modes (unified, side-by-side, context) toggled with d. Keyboard bindings: a allow-once, A allow-always, r reject-once, R reject-always. Permission decisions are persisted via PermissionService. (#996)

• TUI — Actor thought block rendering: ThoughtBlock domain model represents actor reasoning traces with configurable max_lines (default 10), expanded/collapsed state, and helper methods for truncated/full content. ThoughtBlockWidget renders thought blocks with muted styling and a space-bar toggle. (#1001)

• ACMS — UKO runtime operationalized: Three new services complete the Universal Knowledge Ontology runtime per spec §185:

  • UKOQueryInterface — typed interface for ACMS context strategies to query UKO classification data (layer, primary type, implicit relations).
  • UKOInferenceEngine — semantic analysis producing implicit triples (uko:implicitSiblingOf, uko:implicitContains, uko:implicitDependsOn) with confidence 0.7.
  • UKOGraphPersistence — serialises/restores UKO graph state via JSON or in-memory backends, satisfying the "persists across restarts" requirement. UKOIndexer.index_graph() now runs inference and populates uko:layer triples for all four ontology layers. (#891)

• ACMS — Pipeline Phase 2 protocol aliases: Spec-aligned Protocol type aliases added for all Phase 2 (Fragment Fusion) pipeline component interfaces: FragmentDeduplicatorProtocol, DetailDepthResolverProtocol, FragmentScorerProtocol, BudgetPackerProtocol, FragmentOrdererProtocol. (#540)

• Resource — DevcontainerHandler protocol completion: Four previously missing protocol methods implemented on DevcontainerHandler: delete() (uses devcontainer exec rm -rf), list_children() (uses devcontainer exec ls -1), diff() (content-hash comparison), and create_sandbox() (delegates to BaseResourceHandler with lazy activation). All methods return graceful failure results for missing or stopped containers rather than raising. (#1242)

• Resource — DatabaseResourceHandler CRUD and checkpoint methods: Full CRUD and checkpoint implementation for both SQLite and remote database types. read() queries sqlite_master for schema; write() executes SQL statements; delete() executes DROP TABLE IF EXISTS; list_children() lists tables/views; diff() compares schemas via content hash; create_checkpoint() creates a SQLite SAVEPOINT; rollback_to() executes ROLLBACK TO SAVEPOINT. Remote database operations return not-supported results gracefully. (#1241)

• Estimation lifecycle hook: actor.default.estimation config key wired as fallback for plan estimation actor selection. The Strategize-to-Estimate lifecycle hook in PlanLifecycleService now invokes the estimation actor, stores EstimationResult on the plan, populates plan.cost_estimate_usd, and emits a PLAN_ESTIMATION_COMPLETE domain event. Estimation failures are informational only and never block the Execute transition. (#1310)

• Events — user_identity field on DomainEvent: All domain events now carry an optional user_identity field propagated through the full event pipeline (event bus → audit subscriber → audit log). (#1257)

• Events — PLAN_APPLIED enriched with changeset statistics: PlanApplyService.apply_with_validation_gate() now computes files_changed, lines_added, lines_removed, resources_modified, and apply_duration_seconds from SpecChangeSet.summary() and passes them to PlanLifecycleService.complete_apply(), which includes them in the PLAN_APPLIED event details for SEC7 audit logging. (#716)

• Events — PLAN_CANCELLED enriched with progress context: The PLAN_CANCELLED event now includes progress percentage, completed/total action counts, and resource cleanup context. (#1301)

• Server — agents server serve subcommand: BDD scenarios added to verify that Dockerfile.server uses python -m cleveragents as its ENTRYPOINT and server serve as its CMD. (#1088)

Changed (original 3.7.0)

• agents actor run now takes positional <NAME> and <PROMPT> arguments, aligning with the specification. The previous --prompt/-p option is removed. (#901)

• resource_selection decision type reclassified from Execute-only to phase-agnostic (valid in both Strategize and Execute), aligning with ADR-007 and ADR-033. (#931)

• SandboxManager.commit_all() is now an all-or-nothing atomic operation. On partial failure, already-committed sandboxes are rolled back in reverse (LIFO) order. (#925)

Fixed

• agents session list, session create, and other session subcommands no longer raise AttributeError: 'DynamicContainer' object has no attribute 'db' after agents init. (#554, #570, #680)

• plan execute no longer fails with stale-cache state when run in a separate CLI process from plan use. (#960)

• project context set now commits changes via session.commit() instead of session.flush(), preventing silently lost data. (#745)

• agents action create now accepts --format/-f flag, matching all other action subcommands. (#959)

Unreleased (pre-3.7.0)

• Eliminated redundant fields (excluded_decisions, rollback_tier_depth, child_plans_to_rollback) from CorrectionDryRunReport that duplicated data already present in the embedded CorrectionImpact object. Consumers now access these values via report.impact.excluded_decisions, report.impact.rollback_tier_depth, and report.impact.affected_child_plans respectively. Updated CorrectionService.generate_dry_run_report(), Behave step definitions, and Robot Framework helpers to use the canonical impact sub-object. (#1087)

• Added a context-sensitive TUI help panel overlay toggled by F1, with help content that varies for main-screen, slash-command, reference, and shell prompt modes. Updated Behave and Robot coverage for help-panel rendering and mode switching. (#1013)

• Added direct BDD coverage for _fast_init_or_upgrade early-return behavior, template-copy/fallback delegation paths, and the existing-empty-DB branch in features/fast_init_upgrade.feature. Uses race-safe temp-path allocation (mkstemp/mkdtemp) throughout new fast-init test steps. (#733)

• Added get_hover and get_definitions methods to LspClient and LspRuntime, completing the functional LSP runtime (Epic #824). LspClient.get_hover() sends textDocument/hover and returns the hover result dict. LspClient.get_definitions() sends textDocument/definition and handles Location, Location[], and LocationLink[] responses. LspRuntime wrappers add input validation, file reading, language detection, and 1-based to 0-based line/column conversion. Tool adapter now dispatches HOVER and DEFINITIONS capabilities to the runtime instead of raising LspNotAvailableError. Includes 10 Behave BDD scenarios. (#824)

• Expanded the TUI slash command overlay catalog to include 67 commands across 14 groups, aligned with the specification command reference for session, persona, scope, plan, project, registry/config, context, and utility flows. Added Behave coverage for command and group cardinality plus representative command presence checks. (#1002)

• Strengthened WF02 trusted-profile integration coverage for automated test generation. The helper now validates and incorporates mocked provider output (instead of discarding it), asserts all WF02 invariant conventions (test-only paths, test_<module>.py naming, and fixture/conftest usage), verifies user-facing plan artifacts dispatch behavior, and adds explicit negative guardrail tests for absolute/traversal/non-tests destinations. Also narrowed Ruff suppression scope in the WF02 helper. (#766)

• Added TDD bug-capture tests for bug #1025 — plan correct auto-resolve fails in isolated E2E environments. Two Behave BDD scenarios (@tdd_bug @tdd_bug_1025 @tdd_expected_fail) verify that _resolve_active_plan_id() finds an Execute/COMPLETE plan when --plan is omitted. Two Robot Framework integration tests exercise the same path in a subprocess context. Tests simulate the divergent- container condition (fresh CLEVERAGENTS_HOME with empty database). ASV benchmark measures active-plan filtering overhead. (#1035)

• Added missing LspServerConfig model fields per specification: description (max 1000 chars), transport (LspTransport enum with stdio/tcp, default stdio), initialization (dict for LSP initializationOptions), and workspace_settings (dict for workspace/didChangeConfiguration). Updated agents lsp show Rich output to display new fields. All fields have defaults for backward compatibility. Includes 20 Behave scenarios and 5 Robot tests. (#835)

• Added E2E test for Workflow Example 18: Container with Remote Repo Clone (trusted profile). Introduces the new --clone-into CLI flag on resource add for container-instance and devcontainer-instance resources (format: REPO_URL:CONTAINER_PATH), with input validation and type restriction. Exercises two-step project creation and linking, plan-level --execution-environment with --execution-env-priority fallback, and full plan lifecycle including container commit/push verification on apply. (robot/e2e/wf18_container_clone.robot, src/cleveragents/cli/commands/resource.py) (#764)

• Fixed execution environment resolution to honour project-level override (precedence level 2). Threaded plan_env and project_env through ToolCallRouter, ToolCallingRuntime, and PlanExecutionContext so the resolver receives project-level execution environment values stored in ContextConfig.execution_environment. (#1080)

• Added E2E test for Workflow Example 12 — large-scale hierarchical feature implementation (supervised profile). Covers 4-project setup with per-project invariants, spec-compliant action YAML (estimation_actor, invariant_actor, automation_profile: cautious, action-level invariants), all-project plan use, hierarchical tree inspection, plan correct (append mode) on non-root decision, phased lifecycle-apply, and terminal-state verification via JSON status. Dynamic actor selection and UUID-suffixed names for CI safety. Known limitations: plan prompt not yet implemented as CLI subcommand, action --arg omitted due to UNIQUE constraint bug, validation registration omitted pending independent validation. (#758)

• Added E2E test for Workflow Example 17: explicit container with directory mount using trusted automation profile. Exercises container-instance resource registration, project link-resource, execution environment setting via project context set, plan-level execution-env-priority override via plan use, and full plan lifecycle with dynamic actor selection. Includes TDD bug-capture tests for deferred acceptance criteria: dual mount registration (#1078), project-level execution-env-priority (#1079), and precedence level 2 resolution (#1080). (robot/e2e/wf17_explicit_container.robot) (#763)

• Added correction_attempts table per specification DDL with CorrectionAttemptModel ORM, CorrectionAttemptRecord domain model, CorrectionAttemptRepository CRUD layer, Alembic migration, and CorrectionAttemptState enum. Repository update_state() accepts typed CorrectionAttemptState enum and datetime parameters and enforces the spec lifecycle (pending → executing → complete|failed) via InvalidCorrectionStateTransitionError. CorrectionAttemptRecord.guidance validates non-empty with max_length=10_000. created_at column includes spec-aligned server_default; to_domain() normalises naive timestamps to UTC. State transition validation extracted to domain-level validate_correction_state_transition() function with CORRECTION_ATTEMPT_VALID_TRANSITIONS and CORRECTION_ATTEMPT_TERMINAL_STATES constants. update_state() rejects completed_at on non-terminal transitions. Improved FK-violation error messages in create() and update_state(). Normalised timestamp format in from_domain() to millisecond precision (SS.mmm) matching SQLite server_default strftime('%f') output for consistent string-based ordering. CORRECTION_ATTEMPT_VALID_TRANSITIONS and CORRECTION_ATTEMPT_TERMINAL_STATES now use typed CorrectionAttemptState enum keys/values. Updated repository module docstring tables. from_domain() normalises timestamps to UTC via astimezone(UTC) before formatting, preventing silent data loss for non-UTC datetimes. update_state() auto-sets completed_at when transitioning to terminal states if not explicitly provided. CorrectionAttemptRecord plan_id and original_decision_id validators now return stripped values, preventing whitespace-padded IDs from causing FK lookup failures. Added new domain exports to __init__.py __all__. Aligned update_state() completed_at timestamp to millisecond precision for consistency. Improved FK-violation error message in update_state() to avoid misleading reference when new_decision_id is None. Removed unnecessary session.rollback() in read-only repository methods (get(), list_by_plan()) for consistency with other repos. Added created_at and completed_at Pydantic validators on CorrectionAttemptRecord to normalise naive datetimes to UTC, preventing ValueError in from_domain() astimezone() calls. Added defensive enum coercion in CorrectionAttemptModel.to_domain() with warning-level logging for invalid mode/state DB values, consistent with LifecyclePlanModel.to_domain() pattern. Moved CorrectionAttemptState from TYPE_CHECKING-only to runtime import in the repository module, removing redundant in-method import. Changed original_decision_id FK from CASCADE to RESTRICT matching the spec DDL default and the codebase convention for non-dependency FK references to decisions, preserving correction audit trail when decisions are cleaned up. Added new_decision_id strip-and-validate field validator matching the pattern used for plan_id and original_decision_id. Added input validation for new_decision_id in update_state() rejecting empty and whitespace-only values per CONTRIBUTING.md argument validation guidelines. Fixed BDD mode-validation scenario to use dedicated Then step with field-level assertion instead of reusing guidance error step. Moved new_decision_id and archived_artifacts_path argument validation in update_state() before any ORM row mutations per CONTRIBUTING.md early-validation guidelines, preventing dirty session state on validation failure. Added archived_artifacts_path empty/whitespace-only rejection in update_state() matching the new_decision_id validation pattern per CONTRIBUTING.md argument validation guidelines. 43 BDD scenarios and 5 Robot integration tests including cascade deletion, terminal-state rejection, failed-path transition, guidance validation, max-length boundary, min-length boundary, not-found update, FK-violation update, completed_at guard, timezone normalization, archived_artifacts_path round-trip, delete-in-complete- state, cross-plan list isolation, auto-set completed_at on terminal transition, FK violation on create, invalid mode rejection, whitespace/empty new_decision_id rejection, combined field update, self-transition rejection, and empty/whitespace archived_artifacts_path rejection. Fixed update_state() bug where archived_artifacts_path was stored without stripping leading/trailing whitespace, unlike new_decision_id which correctly used the stripped value. Extracted SQLITE_TIMESTAMP_MS_LEN constant and format_sqlite_timestamp() helper for millisecond-precision timestamp formatting, used by both from_domain() and update_state(). Changed InvalidCorrectionStateTransitionError base class from DatabaseError to BusinessRuleViolation per CONTRIBUTING.md exception semantics (state transition is a business rule, not a database error). Changed new_decision_id FK from SET NULL to RESTRICT matching the spec DDL default (no ON DELETE clause) and consistent with original_decision_id. Changed update_state() input validation for new_decision_id and archived_artifacts_path from DatabaseError to ValueError per CONTRIBUTING.md argument validation guidelines. Defensive to_domain() coercion now defaults corrupted state to failed (terminal) instead of pending, preventing re-execution of completed/failed corrections with corrupted DB values. 45 BDD scenarios (was 43) with new RESTRICT FK test for original_decision_id and stronger cross-plan isolation test. Added ORM-level relationship(cascade="all, delete-orphan") on LifecyclePlanModel for CorrectionAttemptModel, consistent with all other v3_plans child tables, ensuring ORM-level cascade deletes work even when SQLite FK enforcement is disabled. Added defensive to_domain() coercion for corrupted guidance column (defaults to "[corrupted]" with warning log), consistent with existing mode/state coercion pattern. Added ValueError guard in format_sqlite_timestamp() rejecting naive datetimes per CONTRIBUTING.md fail-fast argument validation. Fixed update_state() to defensively handle corrupted DB state values (coerces to failed terminal with warning log), consistent with to_domain() defensive coercion pattern. Strengthened RESTRICT FK BDD assertion to verify exception type (IntegrityError/DatabaseError) instead of only checking presence. Split multi-When/Then cross-plan isolation BDD scenario into idiomatic single-When/Then scenarios. 53 BDD scenarios (was 45) with new defensive to_domain() coercion tests (corrupted mode/state/guidance), format_sqlite_timestamp() naive datetime rejection, domain model naive datetime normalisation, and corrupted DB state handling in update_state(). (#920)

• Hardened automation profile configuration validation after the task-flag rename: AutomationProfile now rejects unknown top-level fields instead of silently ignoring them, and raises an actionable ValueError listing the required renames when legacy auto_* keys are supplied (instead of a generic Pydantic "Extra inputs are not permitted" error). Updated automation profile schema and documentation references (specification, ADRs, and reference docs) to the task-type field names, added BDD coverage for rejecting legacy threshold keys in automation-profile add, restored docs-schema parity for optional guards profile configs, aligned the m5_001 migration header metadata text with its actual revision chain, updated M6 fixture files to use the spec-defined field names, added phase-transition semantic bridge comments in PlanLifecycleService. Restored categorised CLI automation-profile show output to match the specification (Phase Transitions / Decision Automation / Self-Repair / Execution Controls), added missing access_network field to spec show output examples, aligned ADR-017 and reference doc descriptions with the specification's Automatable Tasks table (all 11 fields), and extended the repository roundtrip test to assert all 11 threshold fields. Fixed benchmark _make_profile() helper passing safety fields as top-level kwargs instead of via SafetyProfile sub-model (incompatible with extra="forbid"). Aligned CLI JSON/YAML output structure for automation-profile show with the specification's grouped format (phase_transitions, decision_automation, self_repair, execution_controls). Moved safety boolean fields into the Execution Controls section of Rich output per spec examples. Reverted auto profile description to "Fully automatic except apply" per specification. Added comprehensive field-name mapping table to automation_profile.py module docstring documenting the old phase-transition names to new spec task-type names correspondence and added cross-reference in AutonomyController._get_threshold() docstring. (#902)

• Added TDD bug-capture tests for bug #1141 — session create does not persist into subsequent session list output. Added a Behave scenario and Robot E2E test with required tags (@tdd_bug, @tdd_bug_1141, @tdd_expected_fail / tdd_bug, tdd_bug_1141, tdd_expected_fail) to assert create→list should show one session. The underlying assertion currently fails and is intentionally inverted until bug #1141 is fixed. (#1142)

• Fixed project context set missing --execution-env-priority flag. Setting is persisted and displayed by project context show. Project-level priority propagates to plan use when no plan-level override is specified. (#1079)

• Added Robot Framework integration test for Specification Workflow Example 5: Database Schema Migration with Safety Nets. 7 test cases exercising review automation profile, custom local/postgres-db resource type with transaction_rollback sandbox and spec-matching cli_args (host/port/database/ schema), project-resource linking, custom skill with 3 database tools, action with 4 typed args and 4 invariants, checkpoint creation/rollback via CheckpointManager, 5-phase sequential SubplanService.spawn with fail-fast, and plan lifecycle through strategize-to-execute. (#769)

• Implemented --mount flag on resource add container-instance. Supports resource-reference mounts (--mount local/api-repo:/workspace) and host-path mounts (--mount /var/config:/config:ro). Multiple --mount flags can be specified. Mount info is persisted as JSON in resource properties and displayed by resource show. (#1078)

• Added TDD bug-capture tests for #1078 — resource add container-instance missing --mount flag. Three Behave scenarios prove the --mount flag is not recognised. Uses @tdd_expected_fail until fix is merged. (#1099)

• Added WF03 plan prompt and confidence-threshold pausing tests. Behave BDD scenarios and Robot Framework integration tests exercise plan prompt via the A2A facade dispatch path (S15822) -- verifying guidance propagation -- and verify cautious-profile confidence-threshold pausing (S37262-37367) including a pause-and-resume flow. Facade stub updated to echo guidance text. (#961)

• Added TDD bug-capture tests for bug #1023: CLI commands fail without explicit agents init when CLEVERAGENTS_AUTO_APPLY_MIGRATIONS=true is set. Two Behave BDD scenarios and two Robot Framework integration tests verify that resource add and project create succeed in a fresh environment without prior init. Tests use @tdd_expected_fail until the bug fix is merged. (#1033)

• Added TDD bug-capture tests for bug #1079 — project context set missing --execution-env-priority flag. Six Behave BDD scenarios exercise the CLI path (override, fallback, rejection without --execution-environment, default value, invalid value, and round-trip via context show). Three Robot Framework integration tests cover override acceptance, fallback acceptance, and full persistence round-trip. Tests use @tdd_expected_fail until the fix is merged. (#1100)

• Fixed Robot Framework test mocks for plan correct dry-run and correction subplan helpers to use container.decision_service() instead of the non-existent container.resolve(), matching corrected production code. Activated regression-guard BDD scenarios for plan tree, plan explain, and plan correct. (#647)

• Added the production ACMS skeleton compression stage via DepthReductionCompressor. The pipeline now re-renders inherited parent fragments to overview depths 0-1 using the UKO detail-level map chain, exposes the compressor as the configured builtin, and covers the behavior with BDD scenarios for compressor output and default pipeline wiring. (#919)

• Added TDD bug-capture tests for bug #1076 — use_action() does not propagate automation_profile to Plan. Three Behave BDD scenarios (@tdd_bug @tdd_bug_1076 @tdd_expected_fail) verify the full precedence chain (action, project-scoped config, global default) for automation profile resolution at plan use time. Tests prove the bug exists: the Plan's automation_profile is always None regardless of the Action's profile, project config, or global default. The @tdd_expected_fail tag inverts this to a CI pass until the fix is merged. (#1098)

• Added TDD bug-capture tests for bug #1022 — InvariantService in-memory storage only. Four Behave BDD scenarios and three Robot Framework integration tests verify invariant persistence across simulated CLI process restarts. Tests use @tdd_expected_fail until bug #1022 is fixed. (#1032)

• Added TDD bug-capture test for bug #988 — ReactiveEventBus.emit() swallows exception details. Behave BDD scenario (@tdd_bug @tdd_bug_988 @tdd_expected_fail) captures the missing exception message and traceback in the emit() exception handler. The test subscribes a handler that raises ValueError with a distinctive message and asserts the message appears in the structlog warning log — which currently fails, confirming the bug. The @tdd_expected_fail tag inverts this to a CI pass until the fix is merged. (#1093)

• Added ResourceHandler sandbox and checkpoint lifecycle methods: create_sandbox (idempotent, delegates to SandboxManager), create_checkpoint, rollback_to, and project_access. Frozen dataclass result types (SandboxResult, CheckpointResult, RollbackResult, AccessResult) added to the handler protocol. GitCheckoutHandler uses git tag for checkpoint and git checkout for rollback. FsDirectoryHandler uses shutil.copytree snapshot and clear-and-restore. Default project_access delegates to PermissionService (local mode = always permit). (#836)

• Added 5 missing LSP capabilities to LspCapability enum: HOVER, DEFINITIONS, SIGNATURE_HELP, DOCUMENT_SYMBOLS, WORKSPACE_SYMBOLS. Renamed TYPE_INFO -> HOVER, SYMBOLS -> DOCUMENT_SYMBOLS, FORMAT -> FORMATTING for spec alignment. Updated tool adapter with 11 capability mappings, RENAME schema with new_name parameter, workspace-symbols query schema, and defensive schema validation. Extended initialize() to advertise all 11 capabilities. Fixed workspace_symbols runtime handler to accept query-only input. (#834)

• Added per-phase ACMS context analysis summaries for agents project context inspect/simulate with human-readable metrics (fragment/resource counts, size/tokens, budget utilization), explicit strategize->execute->apply narrowing diagnostics, Robot acceptance verification upgrades, and Behave edge-case coverage for empty, single-resource, multi-resource, and budget-constrained contexts. (#849)

• Added 10,000-file ACMS indexing reliability improvements: configurable runtime timeout bounds propagated through the repository indexing service, utility walker, and CLI (agents repo index --timeout-seconds), plus large-scale verification coverage in Behave and Robot and a dedicated 10K-file indexing benchmark path for regression tracking. (#851)

• Added TDD bug-capture E2E tests for bug #1028 — ACMS indexing pipeline not wired into CLI. Four Robot Framework E2E tests prove ContextTierService starts empty on every CLI invocation. Tests use @tdd_expected_fail until the bug fix is merged. (#1029)

• Added Fix-then-Revalidate orchestration loop for required validations: bounded retry with configurable limits (0--100 per Safety Profile), strategy revision escalation via auto_strategy_revision float threshold, user escalation via needs_user_escalation result flag, and domain events (VALIDATION_FIX_ATTEMPTED, VALIDATION_FIX_SUCCEEDED, VALIDATION_FIX_EXHAUSTED). Validation errors are treated as required failures regardless of mode. Includes auto_validation_fix threshold, per-resource retry tracking, early-exit signalling via None return from FixCallback, event bus circuit breaker with lock-protected failure counter, spec-required validation_summary and final_validation_results fields on the result model, DI container registration per ADR-003, and structured logging via structlog. (#583)

• Implemented real revert-mode re-execution from decision point. CorrectionService.execute_revert now performs checkpoint restoration via CheckpointService, extracts actor_state_ref from the target decision's context snapshot for reasoning rollback, generates a user_intervention decision ID for guidance injection, and signals phase transition to Strategize. Added checkpoint_restored, actor_state_ref, user_intervention_decision_id, and phase_transition_target fields to CorrectionResult. Includes 16 Behave BDD scenarios and 7 Robot Framework integration tests. (#844)

• Added LSP resource types: executable, lsp-server, lsp-workspace, lsp-document with parent/child hierarchy, auto-discovery rules, and handler references. Registered in bootstrap, with YAML configurations, Behave BDD tests (21 scenarios), and Robot integration tests (6 tests). (#832)

• Implemented functional LSP runtime replacing local-mode stubs with real LSP protocol support. StdioTransport manages server subprocesses via JSON-RPC over stdin/stdout. LspClient implements initialize/shutdown/ diagnostics/completions. LspLifecycleManager provides reference-counted instances, health checks, and crash restart. LanguageDiscovery implements 4-layer detection (extension, shebang, UKO, project config). Includes 27 Behave BDD scenarios and 6 Robot integration tests. (#826)

• Added ResourceHandler CRUD and discovery methods: read, write, delete, list_children, diff, and discover_children. Frozen dataclass result types (Content, WriteResult, DeleteResult, DiffResult) added to the handler protocol. GitCheckoutHandler implements all six methods via git plumbing and filesystem operations. FsDirectoryHandler implements all six via pathlib/os/difflib. DevcontainerHandler implements read, write, and discover_children via devcontainer exec. DatabaseResourceHandler inherits NotImplementedError stubs pending connection management. (#827)

• Implemented ACMS context tier runtime promotion/demotion/eviction: auto-promotion on access with configurable threshold (default: 5), time-based staleness enforcement (hot/warm TTL, default: 24h each), budget-based LRU eviction on hot-tier overflow, and tier transition event emission (TIER_PROMOTED, TIER_DEMOTED, TIER_EVICTED) via EventBus. Added context_tier_promotion_threshold, context_tier_hot_ttl_hours, and context_tier_warm_ttl_hours settings with DI wiring of event_bus into ContextTierService. Oversized fragments that exceed the entire hot-tier budget are now redirected to the warm tier with a TIER_DEMOTED event. Promotion to hot falls back to warm when the promoted fragment is evicted by budget enforcement. Event emission is best-effort; a failing event bus no longer breaks tier operations. Added CLEVERAGENTS_CTX_HOT_HOURS env var alias for context_tier_hot_ttl_hours for consistency with the warm-tier alias. Demotion now resets access_count to zero so that demoted fragments must accumulate fresh accesses before re-promotion, preventing staleness enforcement from being immediately undone by a single access. (#821)

• Added byte-size budget enforcement for the ACMS context assembly pipeline. enforce_size_budget() filters context fragments against max_file_size (per-fragment) and max_total_size (cumulative) limits defined in a ContextView. New domain models BudgetViolation and BudgetEnforcementResult provide structured violation reporting. Pipeline integration in ACMSPipeline.assemble() applies enforcement as a pre-filter when a context_view is provided. (#847)

• Added E2E test for Workflow Example 16: devcontainer-driven development with supervised automation profile. Exercises devcontainer auto-detection during resource registration, lazy container build during plan execution, tool invocation routing to container workspace, and apply writing changes back to host filesystem via bind mount. Uses dynamic actor selection (Anthropic/OpenAI) and UUID-suffixed names for parallel CI safety. (robot/e2e/wf16_devcontainer.robot) (#762)

• Breaking (behavioral): SandboxManager.commit_all() is now an all-or-nothing atomic operation per specification line 45938. (#925)

  • On partial failure, already-committed sandboxes are rolled back in reverse (LIFO) order following the standard transaction-log undo pattern.
  • Non-SandboxError exceptions are wrapped in AtomicCommitError (chaining the original as __cause__) with rolled_back_ids and failed_rollback_ids attributes; SandboxError exceptions return a CommitResult with rolled_back / rollback_failed metadata.
  • Non-rollbackable sandboxes (NoSandbox, TransactionSandbox) are committed last in the batch so rollbackable sandboxes can be undone if they fail first. A warning is logged when these types are present.
  • TransactionSandbox.rollback() from COMMITTED now raises SandboxRollbackError (database commits are irreversible) instead of silently reporting success.
  • Extracted shared _fs_utils module (backup_directory, safe_restore, compute_diff) with symlink, permission, and timestamp preservation; replaces duplicated per-class methods.
  • safe_restore uses rename-based swap (both renames are O(1) on the same filesystem) to prevent data loss during restore.
  • Pre-commit backup is created on the same filesystem as the original (avoids cross-device copy overhead); assigned only after backup_directory() succeeds; skipped when no changes detected.
  • backup_directory defers directory permissions and timestamps to a bottom-up post-walk pass, fixing POSIX mtime overwrite; skips non-regular files (FIFOs, sockets, device files) with a warning.
  • CopyOnWriteSandbox and OverlaySandbox commit error handler restores original from pre-commit backup; catches Exception (not just OSError) so unexpected errors also trigger restoration.
  • Rollback from COMMITTED with no backup (no changes applied) is a no-op instead of raising SandboxRollbackError.
  • CopyOnWriteSandbox and OverlaySandbox rollback from COMMITTED resets sandbox copy/merged directory from restored original, preventing stale data from being exposed on re-activation.
  • OverlaySandbox rollback from COMMITTED properly remounts OverlayFS (or re-copies for userspace fallback); raises SandboxRollbackError if unmount fails. No longer double-wraps SandboxRollbackError — inner errors are re-raised directly.
  • OverlaySandbox.get_path() now transitions ROLLED_BACK → ACTIVE for consistency with CopyOnWriteSandbox and the protocol transition table.
  • GitWorktreeSandbox.get_path() now accepts ROLLED_BACK status for consistency with all other sandbox types and the protocol transition table (ROLLED_BACK → ACTIVE).
  • rollback_all now also handles sandboxes in COMMITTED status and catches Exception (not just SandboxError) to ensure all rollbacks are attempted.
  • cleanup_all now catches Exception (not just SandboxError) to prevent a single unexpected error from aborting cleanup of remaining sandboxes.
  • CopyOnWriteSandbox and OverlaySandbox rollback from ACTIVE now uses dirs_exist_ok=True to prevent FileExistsError when rmtree silently fails.
  • cleanup_abandoned now catches Exception (not just SandboxError) so that unexpected errors do not crash the loop and prevent remaining abandoned sandboxes from being cleaned up, consistent with cleanup_all, rollback_all, and _rollback_committed.
  • OverlaySandbox._mount_overlay() and _unmount_overlay() now catch subprocess.TimeoutExpired (in addition to CalledProcessError and OSError), preventing create() from leaving the sandbox in PENDING status and cleanup() from leaving it in a zombie state when mount/umount hangs.
  • OverlaySandbox._mount_overlay() validates that overlay paths do not contain commas, which would corrupt the OverlayFS mount options string.
  • GitWorktreeSandbox.commit() now checks git diff return code so that a failed diff command does not silently skip the merge.
  • safe_restore cleanup of the temporary rollback container now runs in a finally block, preventing a temp directory leak when the rename fails and the exception is re-raised.
  • AtomicCommitError exported from sandbox package __init__.py.

• Aligned plan lifecycle model with specification: ERRORED is now terminal in is_terminal, per-phase state validation enforces APPLIED/CONSTRAINED to APPLY-only and COMPLETE to STRATEGIZE/EXECUTE-only via model validator, COMPLETE docstring clarified as phase-level terminal. Added defensive coercion in database deserialization for legacy invalid phase/state combinations with warning-level logging. Fixed assignment ordering in execute_plan() for consistency with phase-state validator. Updated PlanResumeService docstring to reflect ERRORED terminality. (#918)

• Aligned v3_plans table schema with specification DDL: added effective_profile_snapshot column (TEXT NOT NULL, validated as JSON), made root_plan_id NOT NULL with self-referencing for root plans and explicit RESTRICT FK policy, made automation_profile NOT NULL with default "balanced", and documented the intentional phase default deviation ("action" vs spec "strategize"). Migration backfill correctly resolves root ancestors for child plans at arbitrary hierarchy depth via level-by-level propagation with safety bound. Hardened automation_profile deserialization to catch RecursionError. Hardened effective_profile_snapshot deserialization in to_domain() to gracefully fall back to '{}' on corrupted JSON, preventing a single corrupted row from crashing plan reads. Added RecursionError to effective_profile_snapshot Pydantic validator for consistency with automation_profile deserialization. Validator error message now uses length-only to avoid potential information disclosure. Documented intentional column naming conventions vs spec DDL. Migration orphan-row fallback now logs affected row count. Documented FK ondelete policy drift between ORM and migrated schemas. Documented automation_profile dual-format storage semantic. Added TypeError to effective_profile_snapshot deserialization exception list in to_domain() for consistency with the Pydantic validator. Extracted default automation profile name to a module-level constant (DEFAULT_AUTOMATION_PROFILE) to reduce sentinel duplication across models.py and repositories.py. Migration cycle-detection now logs affected plan_id values (truncated to first 50) before the orphan fallback runs. Migration SQL statements uniformly use sa.text() for consistency. Centralised automation-profile serialisation into LifecyclePlanModel._serialize_automation_profile() to eliminate duplication between from_domain() and LifecyclePlanRepository.update(). Moved root_plan_id self-reference resolution from from_domain() into a PlanIdentity model_validator so the domain model is consistent with the DB NOT NULL constraint before and after persistence. Used explicit is not None check in _serialize_automation_profile() for consistency with the explicit-None-check convention used elsewhere in this commit. (#921)

• Fixed shell=True subprocess usage in cli_coverage_steps.py by replacing with shlex.split() and shell=False for defense-in-depth command injection prevention, consistent with the existing pattern in cli_plan_context_commands_steps.py. (#734)

• Added TDD bug-capture test for bug #987: AutomationProfileRepository session leak. Four Behave BDD scenarios verify that upsert() and delete() close the database session in auto_commit mode, capturing the missing session.close() in a finally block. Tests use @tdd_expected_fail until the bug fix is merged. (#1092)

• Added ACMS Backend Abstraction Layer (BAL) protocol definitions and in-memory stub implementations. Defines TextBackend, VectorBackend, and GraphBackend protocols with frozen result dataclasses (TextResult, VectorResult, GraphResult). In-memory stubs (InMemoryTextBackend, InMemoryVectorBackend, InMemoryGraphBackend) validate arguments and return empty results for development and testing. Backends registered as configurable singletons in the DI container with provider selection via override_providers(). Includes Behave BDD tests (35 scenarios), Robot Framework smoke tests, ASV benchmarks, and reference documentation. (#498)

• Added TDD bug-capture tests for #1024 — SQLite DB URL resolves to CWD instead of CLEVERAGENTS_HOME. Behave BDD scenarios (@tdd_bug @tdd_bug_1024 @tdd_expected_fail) verify that the default database_url resolves inside CLEVERAGENTS_HOME, not the current working directory. Includes Robot Framework integration tests with a helper script exercising the same resolution path via subprocess. (#1034)

• Added integration Robot Framework test for Specification Workflow Example 7: CI/CD Integration — Automated PR Review and Fix. Exercises the ci automation profile (headless, non-interactive) covering: ci-profile configuration (automation-profile, format, log level), idempotent resource and project registration with duplicate-detection assertions, three validation tools (ci-lint, ci-typecheck, ci-tests) registration and resource attachment via ToolRegistryService, action creation with typed arguments and invariants per spec Step 2, plan lifecycle with explicit phase/state transition assertions across all phases (strategize, execute, apply) plus terminal applied and cancelled path checks, and JSON output structure verification including plan_id, phase, state, action, projects, and arguments fields. (robot/wf07_cicd_integration.robot, robot/helper_wf07_cicd.py) (#771)

• Added integration Robot Framework test for Specification Workflow Example 14: Server Mode — Team Collaboration. Exercises server mode configuration, config-registry diagnostics, namespace management, action publishing with namespaced actor references and supervised profile metadata, shared action consumption via use_action() with required arguments and project links, and namespace + phase plan monitoring using mocked LLM providers and in-memory domain services (CLEVERAGENTS_TESTING_USE_MOCK_AI=true). (robot/wf14_server_mode_integration.robot, robot/helper_wf14_server_mode.py) (#778)

• Added volatile in-memory audit_log to ReactiveEventBus — every emitted DomainEvent is appended to a volatile in-memory log accessible via the audit_log property (defensive copy). Emit ordering now follows the specification: RxPY stream push, then audit append, then handler dispatch. Reactive and logging event buses now isolate stream/handler failures so one subscriber cannot block audit recording or downstream subscribers. The reactive stream now returns a read-only observable view (preventing direct on_next() bypass), and ReactiveEventBus supports explicit in-memory retention controls via max_audit_log_size and clear_audit_log(). Includes expanded Behave and Robot integration coverage, 5 ASV benchmark suites, and vulture_whitelist.py entry. (#587)

• Breaking (CLI): agents actor run now takes positional <NAME> and <PROMPT> arguments, aligning the command signature with the specification. The previous --prompt/-p option is removed. --config/-c is preserved as an optional fallback that overrides registry-based name resolution (spec deviation documented in _resolve_actor.py). Shared resolution logic extracted to _resolve_actor.py with yaml.safe_dump, early name validation, input sanitisation, resilient atexit-based temp file cleanup, and graceful error handling for missing actors, empty config data, and non-serialisable config blobs (without exposing serializer internals in user-facing errors). Comprehensive BDD and Robot Framework tests cover all resolution paths and edge cases. (#901)

• Fixed list_actions() to query the database when persistence is enabled so that actions created by previous CLI invocations are visible. Falls back to the in-memory cache on database errors or when no Unit of Work is wired. Added ActionRepository.list_all() for unfiltered action listing. (#760)

• Added TDD bug-capture test for bug #1080 — execution environment resolution ignores project-level override. Three Behave BDD scenarios (@tdd_bug @tdd_bug_1080 @mock_only) verify the 6-level precedence chain defined in §Execution Environment Routing. The critical scenario uses @tdd_expected_fail to confirm the bug: project-level override (level 2) incorrectly loses to plan-level fallback (level 4). Two regression guard scenarios verify existing correct behaviour (plan override vs project override, project override vs host default). (#1101)

• Added TDD bug-capture tests for bug #1038 — agents validation add missing --required/--informational flags. Four Behave BDD scenarios (@tdd_bug @tdd_bug_1038 @tdd_expected_fail) verify that the add command accepts --required and --informational flags and that --required overrides the YAML config mode. Tests use @tdd_expected_fail until the bug fix is merged. (#1102)

• Fixed execution environment resolution to honour project-level override (precedence level 2). Threaded plan_env and project_env through ToolCallRouter, ToolCallingRuntime, and PlanExecutionContext so the resolver receives project-level execution environment values stored in ContextConfig.execution_environment. (#1080)

• Added BuiltinAdapter class and MCP automatic resource slot creation. BuiltinAdapter wraps register_file_tools/register_git_tools/register_subplan_tool into a unified adapter interface. McpAdapter.infer_resource_slots() analyzes tool input schemas to detect file/directory/repository parameters. (#882)

• Added large-project scaling performance tests with ASV benchmarks for context assembly, execution throughput, and project scaling. Includes Behave BDD scenarios (78 scenarios, 200 steps), Robot Framework tests, and baseline threshold fixtures. (#576)

• Added overlay filesystem sandbox strategy with real OverlayFS support and userspace copy-tree fallback. Includes lifecycle management, diff computation, and sandbox factory registration. (#880)

• Added Kubernetes Helm chart in k8s/ directory for server deployment. Chart includes Deployment, Service, Ingress (with TLS termination), ConfigMap, ServiceAccount, Secrets, and optional Redis subchart for multi-instance session affinity. Added Dockerfile.server for ASGI server containerization with multi-stage build, non-root user, and pinned uv version. Includes deployment README with configuration reference and quick-start instructions. (#928)

• Added CLI polish infrastructure: shared constants.py (exit codes, format constants), centralized errors.py (cli_error, cli_not_found, cli_warning), and completion command for shell tab-completion generation. (#861)

• Added tool-level execution environment preferences with NONE, REQUIRED, PREFERRED, and SPECIFIC modes. ToolRunner routes tool execution based on preference mode with caller-override precedence. (#879)

• Added Robot Framework integration test suite for Specification Workflow Example 4: Multi-Project Dependency Update. 8 test cases exercising supervised automation profile with 4 projects, child plan spawning, dependency-ordered execution, and coordinated apply. Uses mocked LLM providers via CLEVERAGENTS_TESTING_USE_MOCK_AI. (#768)

• Added TDD bug-capture tests for #969 — plan correct expects decision_id but M3 acceptance test passes plan_id. Behave BDD scenarios (revert and append modes) and Robot Framework integration tests verify that request_correction is called with the root decision ID when a plan_id is given as the first positional argument. Tests use @tdd_expected_fail until the bug fix is merged. Shared mock fixtures extracted to features/mocks/tdd_plan_correct_plan_id_fixtures.py. (#979)

• Added TDD bug-capture tests for bug #968: plan explain expects a decision_id but the M3 acceptance test passes a plan_id. Two Behave BDD scenarios (@tdd_bug @tdd_bug_968 @tdd_expected_fail) verify the fixed behaviour — plan explain <plan_id> succeeds (rc=0) and displays decision details. Includes Robot Framework integration tests with a helper script exercising the same CLI path via subprocess, and step definitions following established patterns. (#978)

• Added TDD bug-capture tests for bug #967 — plan execute phase processing. Tests exercise the CLI orchestration layer via CliRunner (Behave) and replicated CLI logic (Robot) to verify that plan execute correctly handles plans in Strategize/QUEUED state by running run_strategize() before transitioning. Includes four Behave scenarios and four Robot integration test cases covering CLI execute from QUEUED, full lifecycle orchestration, positive control, and auto-discovery of QUEUED plans. (features/tdd_plan_execute_phase_processing.feature, robot/tdd_plan_execute_phase_processing.robot) (#977)

• Breaking (behavioral): resource_selection decision type reclassified from Execute-only to phase-agnostic (valid in both Strategize and Execute). DecisionType.RESOURCE_SELECTION now appears in both STRATEGIZE_TYPES and EXECUTE_TYPES. Code relying on is_strategize_type or is_execute_type returning False for resource_selection will see different results. Reclassification aligns with ADR-007 L72 and ADR-033 L74 which permit resource selection during planning. (#931)

• Added E2E test for Workflow Example 4: Multi-Project Dependency Update (supervised profile). Exercises the full supervised plan lifecycle across 4 git repositories (common-lib + 3 services), validates child plan spawning, dependency-ordered execution and apply, per-project validation attachment, and automation profile enforcement via the agents plan use CLI. (#750)

• Added ResourceHandler CRUD and discovery methods: read, write, delete, list_children, diff, and discover_children. Frozen dataclass result types (Content, WriteResult, DeleteResult, DiffResult) added to the handler protocol. GitCheckoutHandler implements all six methods via git plumbing and filesystem operations. FsDirectoryHandler implements all six via pathlib/os/difflib. DevcontainerHandler implements read, write, and discover_children via devcontainer exec. DatabaseResourceHandler inherits NotImplementedError stubs pending connection management. (#827)

• Added E2E test for Workflow Example 5: Database Schema Migration with Safety Nets (review automation profile). Exercises custom resource type registration (resource type add), custom skill creation with spec-aligned database tools (query_db, execute_migration, backfill_column), phased child plan execution verification via plan tree, checkpoint-based rollback via plan rollback, and post-apply migration content verification. (robot/e2e/wf05_db_migration.robot) (#751)

• Implemented 6-level execution environment precedence chain per spec lines 19324-19386. Plan/project environments now support override vs fallback priority modes. Level 3 (nearest-ancestor devcontainer) auto-detection integrated. Added execution_env_priority field to ContextConfig. New resolve_with_precedence() API on ExecutionEnvironmentResolver. Legacy 4-level resolve() preserved for backward compatibility. Includes 13 new Behave scenarios. (#877)

• Added built-in deferred virtual resource types: remote, submodule, and symlink with equivalence metadata rules for cross-repo and cross-layer identity tracking. Registry bootstrap includes deferred virtual types but hides them from resource add scaffolding (user_addable: false). Includes YAML configurations, Behave BDD tests (47 scenarios), Robot Framework integration tests, ASV benchmarks, and reference documentation. (#331)

• Enhanced CorrectionService subtree isolation: analyze_impact() now populates excluded_decisions and rollback_tier_depth; added compute_rollback_tier(), validate_subtree_isolation(), and dry-run report enhancements with tier-0 root-targeted warnings. Fixed status state-machine regression in execute_revert() where analyze_impact() overwrote status back to ANALYZING; execute_revert() now transitions through ANALYZING before EXECUTING for correct lifecycle ordering. Fixed validate_subtree_isolation() to check structural-only BFS for sibling invariant so influence-DAG-caused sibling reachability is not misreported as a violation. Fixed false-positive cycle-detection warnings from convergent (diamond) topologies by using a global enqueued set in BFS instead of per-node seen_this_round. Added dry_run enforcement guard in _assert_executable() to prevent execution of dry-run-only corrections per spec (§ plan correct --dry-run). Added terminal-state guard in analyze_impact() to reject re-analysis after execution. Added mode validation in execute_revert()/execute_append() to prevent mode-mismatched execution. Fixed generate_dry_run_report() to preserve request status (dry-run is non-mutating). Fixed tier-0 warning to only trigger when target is genuinely in the structural tree. Fixed _collect_all_decisions() to always include the target decision in the universe. Improved cycle-detection log message accuracy. Extracted cost/time estimation constants. Fixed generate_dry_run_report() to use try/finally for status restoration so that an exception during analyze_impact() does not leave the request stuck in ANALYZING status. Promoted terminal-status set to a module-level _TERMINAL_STATUSES frozenset constant. Review-cycle fixes: fixed generate_dry_run_report() to also restore _impacts dict (not only status) so dry-run is fully non-mutating; fixed tier-0 warning to compare against the actual root via _find_root() rather than key-in-tree heuristic, preventing false warnings for forest topologies; fixed BFS cycle detection to log at enqueue time so the warning is reachable (previously dead code due to redundant visited vs enqueued sets); added _EXECUTABLE_STATUSES module-level frozenset for _assert_executable() and cancel_correction(); added _MAX_TREE_NODES guard in analyze_impact() to reject pathologically large inputs; execute_revert() now reuses cached impact from _impacts when available to avoid redundant O(V+E) recomputation; execute_append() now transitions through ANALYZING before EXECUTING for consistent lifecycle across both modes; event emission (_emit_correction_applied) now includes attempt_id and logs failures at error level; added max_length=10000 to CorrectionRequest.guidance field; moved status transition after attempt creation in both execution paths. Includes Behave BDD scenarios (influence DAG, append mode, negative isolation validation, dry-run enforcement, execute-revert end-to-end, status guard, mode mismatch, single-node tree, terminal state guard, exact-match affected count, convergent diamond DAG topology, dry-run exception recovery, execute-revert with influence edges, DAG-only nodes in excluded set), Robot Framework integration tests, and updated dry-run report model fields. (#845)

• Added deferred physical resource types for git object taxonomy (git, git-remote, git-branch, git-tag, git-commit, git-tree, git-tree-entry, git-stash, git-submodule) and filesystem link types (fs-symlink, fs-hardlink). All types are built-in, physical, and auto-discovered with bounded scan_depth. Updated fs-directory child types and auto-discovery. Updated git-checkout child types. Includes YAML configs, Behave BDD tests, Robot tests, and ASV benchmarks. (#330)

• Added TDD bug-capture tests for #932 (plan apply missing --yes flag). (#950)

• Modified auto_progress() to complete the Apply phase immediately after transitioning from Execute to Apply, since Apply is a metadata transition with no LLM processing. This ensures plan execute drives the plan to the terminal applied state when the automation profile permits (ci, full-auto profiles with auto_apply < 1.0). Extracted _complete_apply_if_queued() helper that consolidates the Apply-completion pattern (start_apply + complete_apply) into a single method with error recovery (calls fail_apply on failure) and async-job guard (skips inline completion when async execution is enabled to avoid orphaning enqueued jobs). Used by auto_progress(), lifecycle_apply_plan(), and try_auto_run(). Added PlanLifecycleService.try_auto_run() that drives plans through all lifecycle phases (Strategize → Execute → Apply) when automation-profile thresholds allow automatic progression; a threshold of 1.0 stops the plan at that phase boundary for human approval. Fixed lifecycle-apply CLI leaving plans stuck in apply/queued without completing. The command now calls _complete_apply_if_queued() when the plan is in Apply/queued, driving it to the terminal applied state. Fixed stale RICH output in lifecycle_apply_plan that printed "Plan is now in Apply phase (queued)" after the plan had already reached terminal applied state; now branches on plan.is_terminal. Fixed SQLite UNIQUE constraint violation in LifecyclePlanRepository.update(): added session.flush() after clear() on child collections (project_links, arguments, invariants) before re-inserting rows. Added state alias in _plan_spec_dict() JSON output for spec §Example 7 jq compatibility. Updated plan execute and lifecycle-apply reference documentation. (src/cleveragents/application/services/plan_lifecycle_service.py, src/cleveragents/cli/commands/plan.py, src/cleveragents/infrastructure/database/repositories.py, docs/reference/plan_cli.md) (#753)

• Fixed plan execute CLI failing with "Plan is not in an executable state (current: strategize/queued)" after strategize completed successfully. Root cause: _get_plan_executor() created a second PlanLifecycleService Factory instance with its own in-memory _plans cache. After the executor's run_strategize() advanced the plan to execute/queued (via auto_progress), the CLI handler's separate service instance returned stale strategize/queued state from its cache. Fix: _get_plan_executor() now accepts an optional lifecycle_service parameter; the plan execute handler passes its own service instance so both share the same cache. (src/cleveragents/cli/commands/plan.py)

• Improved type safety: _get_plan_executor() parameter lifecycle_service now typed as PlanLifecycleService | None instead of Any | None. (src/cleveragents/cli/commands/plan.py)

• Added BDD regression test verifying that plan execute CLI handler passes its lifecycle service instance to _get_plan_executor(), preventing stale-cache regressions. (features/plan_lifecycle_cli_coverage.feature)

• Added M5 (v3.4.0) E2E acceptance test suite robot/e2e/m5_acceptance.robot with 21 zero-mock test cases covering context assembly, context policy configuration, budget enforcement, context analysis, 10,000+ file scaling, and plan execution with real LLM calls (openai/gpt-4o-mini). (#745)

• Fixed project context set writing policy changes via session.flush() instead of session.commit(), causing silently lost data on session.close(). (#745)

• Added session_factory DI provider to Container for CLI project-context commands. The four project context subcommands (set, show, inspect, simulate) previously called container.session_factory() which did not exist, causing AttributeError at runtime. (#745)

• Added Google/Gemini API key pattern (AIzaSy...) to secret redaction in redaction.py. (#745)

• Added --skill <SKILL> repeatable flag to agents actor run and actor-run CLI commands. The flag resolves named skills from the Skill Registry at runtime and merges their tools into agents that already have configured tools, enabling ad-hoc skill injection without modifying YAML configuration. Skill resolution uses the DI-provided SkillService singleton; unknown or invalid skill names produce a clear error and exit code 2. (#887)

• Added --execution-env-priority flag to agents plan use command, accepting fallback (default) or override to control execution environment routing precedence per ADR-043. Includes ExecutionEnvPriority StrEnum on the domain model, domain-level model validation (priority requires environment), as_cli_dict() support for both execution_environment and execution_env_priority, database persistence via new columns on LifecyclePlanModel with Alembic migration, and a save_plan() service method to re-persist CLI overrides after plan creation. (#886)

• Added estimation actor support and role-aware actor validation for issue #650.

  • Schema/validation: introduced role_hint and response_format fields, plus role-aware compatibility warnings through shared validation helpers.
  • Preflight/CLI wiring: aligned actor registration and preflight warning paths to use the same warning logic and resolved estimation actor configs before preflight compatibility checks.
  • Examples/docs/tests: added examples/actors/estimator.yaml, updated actor example docs, and expanded Behave/Robot coverage for estimator schema and warning scenarios.
  • E2E helper behavior: aligned M1/M2/M3/M6 integration helper handling so missing OpenAI provider keys in local environments are controlled non-crash outcomes while tracebacks/unexpected internal failures still fail.
  • Runtime enforcement of response_format in provider invocation remains planned and tracked via TODO comments in runtime code. (#650)

• Added interactive TUI persona and input-mode support with a dedicated agents tui entry point and Textual app scaffolding. Personas are now managed as local YAML configs with per-session binding/state, and input handling supports Normal (@ references), Command (/ slash commands), and Shell (! passthrough) flows with picker/overlay components and fuzzy matching primitives. Includes Behave feature coverage for TUI persona/input behavior, Robot TUI smoke validation, and an ASV fuzzy-reference benchmark. (#695)

• Added TDD regression tests for bug #647 (Container.resolve() crash in plan tree, plan explain, and plan correct) using real DI wiring in Behave and Robot. Added regression-guard assertions, cache/singleton cleanup hardening, and targeted issue-648 review follow-ups. (#648)

• Added four CLI-based integration test cases to M5 E2E verification suite for v3.4.0 milestone acceptance criteria validation. Tests exercise project create, resource add git-checkout, project link-resource, and project show via real subprocess calls to python -m cleveragents with per-test workspace isolation. (#496)

• Fixed ProjectResourceLinkRepository.create_link() and remove_link() only calling session.flush() without session.commit(), causing linked resource data to be lost between sessions. Added finally: session.close() to both methods to match the session-factory lifecycle pattern used by all other mutating repository methods. (#496)

• Fixed agents plan execute always using local-only stub actors that returned empty changesets instead of invoking real LLM providers. The CLI command only performed phase transitions (Strategize → Execute) without ever running the PlanExecutor to drive the strategize or execute actors. Added _get_plan_executor() helper that resolves ProviderRegistry from the DI container and constructs LLMStrategizeActor / LLMExecuteActor for real LLM calls. Updated execute_plan CLI to detect plan phase/state and automatically invoke the appropriate actor: strategize actor when the plan is in Strategize/queued, phase transition for Strategize/complete, and execute actor for Execute/queued. Existing mock-based tests remain backward-compatible via duck-typing fallback. New llm_actors.py module provides LLMStrategizeActor (task decomposition) and LLMExecuteActor (code generation) that resolve provider/model actor names to LangChain LLM instances. PlanExecutor.__init__ now accepts optional strategize_actor and execute_actor parameters with stub defaults. (#960)

• Fixed agents action create missing the --format/-f flag. All other action subcommands (list, show, archive) already accepted --format and routed through _print_action(), but create was the only one omitted. Running action create --config action.yaml --format plain previously failed with a Typer unrecognized-option error. Added the fmt parameter to the create() function signature and wired it to _print_action(). (#959)

• Added E2E acceptance test for M2 (v3.1.0): Actor Compiler + Full LLM Integration. Robot Framework test suite robot/e2e/m2_acceptance.robot exercises actor YAML compilation into functional graphs, skill registry, tool lifecycle, and plan execution with a custom actor using real LLM API keys. Test flow: create temp git repo → register custom actor → register resource and project → create action → run full plan lifecycle (use → execute strategize → execute → diff → apply) → verify actor compilation and plan integrity. Uses [Tags] E2E, Skip If No LLM Keys, and flexible structural assertions with expected_rc=None for LLM-dependent commands. (#742)

• Fixed plan execute failing with Error [500] INTERNAL when run in a separate CLI process from plan use. Root cause: start_strategize() built its action registry from the in-memory _actions dict only, missing DB-persisted actions created by prior CLI invocations. The preflight guardrail then rejected the plan with a PreflightRejection that escaped the CLI error handler (extends bare Exception, not CleverAgentsError). Fixes: (1) start_strategize() now loads the plan's action from the persistence layer before preflight checks, (2) execute_plan CLI catches PreflightRejection for user-friendly errors, (3) plan execute runs the execute phase inline so the plan progresses through execute/queued → execute/complete in a single CLI invocation, (4) lifecycle-apply handles plans already auto-progressed to apply/queued by complete_execute(). (src/cleveragents/application/services/plan_lifecycle_service.py, src/cleveragents/cli/commands/plan.py) (#746)

• Added E2E Robot Framework acceptance test for M6 (v3.5.0) autonomy hardening milestone. Exercises session CRUD lifecycle, automation-profile list/show/set, project init with git-checkout resource, A2A plan lifecycle (use, lifecycle-list, status, execute, lifecycle-apply), guard enforcement via automation profiles, and a full autonomy acceptance flow — all via real CLI invocations. LLM-dependent tests skip gracefully when API keys are absent. Hardened shared E2E keywords: safe JSON parsing with multi-object fallback, git return-code checks, special-character-safe API-key detection, IF/ELSE migration from deprecated Run Keyword If, per-test teardowns, and Force Tags. Profile list now verifies all 8 built-in profiles. Session delete confirms removal via re-list. Apply step verifies phase transition. Execute step asserts plan_id in output. JSON-quoted assertions for short profile names ("ci", "auto") prevent false-positive substring matches. Added four new E2E tests covering remaining acceptance criteria: guard enforcement with custom profile (denylist, budget caps, tool-call limits), profile precedence resolution (plan-level overrides global), event queue pub/sub via plan lifecycle state transitions, and hierarchical decomposition verification via plan tree. Post-review hardening (PR #803): LLM-dependent tests now Fail instead of Skip when API keys are present but plan use returns non-zero. Event Queue test (AC-3) uses hard assertions for state transition verification. Hierarchical Decomposition test (AC-6) asserts at least one decision node exists after execution. Guard Enforcement Assertions verify the resolved profile name matches the expected value. Extracted Setup Plan Test Resources keyword to eliminate repeated boilerplate and bring the file under the 500-line limit. Verify Plan In List and Full Flow Apply Step keywords use hard assertions instead of WARN fallbacks. Profile Precedence test documents that action > global precedence requires production wiring not yet present in PlanLifecycleService.use_action. (robot/e2e/m6_acceptance.robot, robot/e2e/common_e2e.resource) (#746)

• Added E2E Robot Framework test for Specification Workflow Example 7: CI/CD Integration — Automated PR Review and Fix. Exercises the ci automation profile (headless, non-interactive) with JSON output and log-level configuration, idempotent resource and project registration with --branch and --description flags, three-validation registration (source/mode/code) with project attachment and project show verification, action creation with spec-aligned name (local/review-pr), complete definition_of_done, invariants, and arguments, plan launch with --arg flags, explicit plan execute for lifecycle progression, plan status terminal-state assertion, plan diff JSON validation, and JSON output verification. Resource/project naming follows spec convention (local/ci-workspace project, local/ci-main resource). Entity creation commands tolerate "already exists" for CI re-runnability. Extract JSON Field keyword handles CLI debug log lines preceding JSON via JSONDecoder.raw_decode(strict=False). Fail-fast expected_rc only where the spec mandates error suppression (2>/dev/null || true); first resource add and project create now assert expected_rc=${0}. Config assertions use stdout-only matching and exact equality for the ci profile value. Project idempotency verified with occurrence count. Empty plan-diff stdout logged as warning. Validation naming aligned with spec (local/ci-lint per §Example 7). All Run Process calls include on_timeout=kill per codebase CI stability standard. Added on_timeout=kill to Run CleverAgents Command and Create Temp Git Repo keywords in common_e2e.resource for consistent timeout handling across all E2E suites. Dynamic actor selection based on available API keys (same pattern as m6_acceptance.robot) avoids runtime failure when only one provider key is set. Poll Plan Until Terminal keyword now integrated into the CI Plan Launch test case per spec Step 3 polling loop. Replaced local Extract JSON Field with shared Safe Parse Json Field from common_e2e.resource. Added Force Tags E2E and per-test [Teardown] blocks. Added WF07 Suite Setup keyword for database initialisation. Added robot/common_vars.py module placeholder for shared Robot Framework variables. (robot/e2e/wf07_cicd.robot, robot/e2e/common_e2e.resource, robot/common_vars.py) (#753)

• Added E2E Robot Framework test for Specification Workflow Example 14: Server Mode — Team Collaboration. Exercises server mode configuration (server URL, token, namespace), diagnostics, action publishing to team namespace with namespace-scoped listing, actor registration, plan list smoke test, and supervised automation profile verification with threshold field assertions via real CLI with zero mocking. (robot/e2e/wf14_server_mode.robot) (#760)

• Fixed agents session list, agents session create, and other session subcommands raising AttributeError: 'DynamicContainer' object has no attribute 'db' after agents init. Root cause: _get_session_service() called container.db() but no db provider existed. Added a session_service DI provider in container.py that builds the engine, sessionmaker, and auto-committing repositories. Rewrote _get_session_service() to resolve via the container with module-level caching. Added auto_commit parameter to SessionRepository and SessionMessageRepository to prevent resource leaks in CLI context while preserving Unit-of-Work semantics. Unified error handling across all 7 session subcommands. Includes Behave BDD regression scenarios, Robot Framework integration smoke tests, and structlog isolation for parallel test execution. (#554, #570, #680)

• Added Robot Framework E2E acceptance test for M1 (v3.0.0) milestone. Tests the complete plan lifecycle (action create → resource add → project create → plan use → plan execute strategize → plan execute → plan diff → plan apply) with real LLM API keys and no mocking. Gracefully skips when API keys are absent. (#741)

• Added dedicated E2E test infrastructure: new nox -s e2e_tests session running Robot Framework with --include E2E tag filter against robot/e2e/ directory, dedicated CI job with real LLM API key secrets, graceful skip when API keys are absent, and --exclude E2E on the standard integration test session. Includes a minimal smoke test exercising agents --version and agents --help. (#740)

• Implemented tdd_expected_fail tag handling in Robot Framework via a Listener v3 module (robot/tdd_expected_fail_listener.py). Tests tagged tdd_expected_fail that fail have their result inverted to pass (expected failure); tests that unexpectedly pass are reported as failed with guidance to remove the tag. Tag validation enforces tdd_bug + tdd_bug_<N> prerequisites. Includes idempotency guard against double-invocation, explicit SKIP status handling, and a close() hook for clean teardown. Listener is registered in the nox integration_tests and slow_integration_tests sessions. Fixture files are excluded from the main pabot runner via tdd_fixture tag. Includes 9 Robot Framework integration test cases. (#628)

• Added TDD-style failing Behave BDD tests for the session list DI container missing db provider bug. Three scenarios exercise session list, _get_session_service(), and session list --format json through the real DI path. Includes Robot Framework smoke tests and ASV benchmarks. Tests are intentionally failing (@tdd_expected_fail) until the bug fix for #554 is applied. (#631)

• Added TDD-style failing Behave BDD tests for the session create DI container missing db provider bug. Three scenarios exercise session create, session create --actor, and session create --format json through the real DI path. Includes Robot Framework smoke tests and ASV benchmarks. Tests are intentionally failing (@tdd_expected_fail) until the bug fix for #570 is applied. (#630)

• Implemented UKO Layer 2 paradigm vocabulary specializations: Object-Oriented (uko-oo:), Functional (uko-func:), and Procedural (uko-proc:). Added OWL/Turtle class and property definitions for all three paradigms in docs/ontology/uko.ttl. Implemented DetailLevelMapBuilder with insertion and integer reassignment logic for extending parent DetailLevelMaps. ParadigmVocabulary, VocabularyClass, VocabularyProperty, and VocabularyRegistry frozen Pydantic models provide the Python API. Includes Behave BDD tests (60+ scenarios), Robot Framework integration helper, ASV benchmarks for DetailLevelMap operations, and reference documentation. Breaking: DetailLevelMap.effective_levels() now returns MappingProxyType[str, int] (read-only) instead of dict[str, int]; callers that mutated the returned mapping must copy to a dict first. (#575, PR #657)

• Implemented UKO Layer 3 technology-specific vocabulary extensions for Python (uko-py:), TypeScript (uko-ts:), Rust (uko-rs:), and Java (uko-java:). Each vocabulary defines OWL classes, properties, Layer 2 dependencies, and DetailLevelMap insertions per specification lines 44405-44420. Python inserts 3 new depth levels (DECORATED_SIGNATURES, TYPE_STUBS, WITH_TESTS) producing a 15-level effective map; TS/RS/Java extend at SIGNATURES level without new insertions. Includes OWL/Turtle ontology files, ProvenanceInfo model with 2 required fields (source_resource, source_path) and 3 defaulted fields (source_range, valid_from, is_current), build_detail_level_map/resolve_detail_level utilities, and full Behave BDD tests (78 scenarios, 200 steps). (#576)

• Added RepoIndexingService for repository file indexing with incremental refresh, extension-based language detection, SHA-256 content hashing, and token estimation. Supports policy enforcement via include/exclude globs, max file size, and max total size limits from project ContextConfig. Persists index metadata and per-file records to SQLite via RepoIndexModel and IndexedFileModel. Domain models (IndexStatus, FileRecord, IndexMetadata, RepoIndex) are frozen Pydantic v2 with ULID IDs and UTC datetimes. Wired into the DI container. Includes 28 Behave BDD scenarios, 3 Robot Framework integration tests, ASV benchmarks (5 time + 2 track), and reference documentation. (#195)

• Wired retry policies and circuit breakers into the service layer. RetryPolicyConfig and CircuitBreaker models govern per-service retry behaviour (max attempts, backoff strategy, delay bounds, jitter) and circuit breaker protection (failure threshold, recovery timeout, half-open probing, cooldown). ServiceRetryWiring initialises from Settings, creates CircuitBreaker instances per service, and exposes execute()/async_execute() helpers. retry_service_operation decorator adds retry + circuit breaker to any service method via a single annotation. Structured logs are emitted on every retry attempt and when a circuit breaker opens. Retry amplification is prevented by a contextvars nesting guard. Per-service overrides are loaded from the retry_service_overrides JSON config key. Includes Behave BDD unit tests, Robot Framework integration tests, and ASV benchmarks. (#313)

• Added container-aware tool execution and I/O forwarding via ContainerToolExecutor and PathMapper. Tools routed to execution_environment: container are executed inside a provisioned devcontainer with automatic host↔container path mapping, bounded output capture (50 MiB), structured error reporting, and container metadata on the ToolInvocation audit trail. Includes ContainerConfig, ContainerMetadata, ContainerExecutionError, and ContainerTimeoutError domain models, ToolRunner container routing integration, safe environment filtering, symlink/traversal protection, and sync_results_to_host for file-based result retrieval. Covered by Behave BDD scenarios, Robot Framework integration tests, ASV benchmarks, and docs/reference/execution_environment.md. (#515)

• Implemented @tdd_expected_fail tag handling in Behave environment hooks. Added validate_tdd_tags() and should_invert_result() helper functions in features/environment.py. Scenarios tagged @tdd_expected_fail that fail have their result inverted to pass (expected failure); scenarios that unexpectedly pass are reported as failed with guidance to remove the tag. Tag validation enforces @tdd_bug + @tdd_bug_<N> prerequisites. Implemented via Scenario.run() monkey-patch in before_all. Includes 34 Behave BDD scenarios (19 tag-validation, 14 infrastructure, and 1 demo) and 12 Robot Framework integration test cases. (#627)

• Wired AuditService.record() into domain services via EventBus auto-dispatch. Created AuditEventSubscriber that subscribes to 9 security-relevant event types (plan_applied, plan_cancelled, resource_modified, correction_applied, config_changed, entity_deleted, session_created, auth_success, auth_failure) and persists them via AuditService.record() with secret masking applied to all audit log details (always show_secrets=False). Subscriber enriches audit entries with session_id and correlation_id from the domain event for traceability. Wired PlanLifecycleService to emit PLAN_APPLIED and PLAN_CANCELLED events with all project names in event details. Added 5 new EventType enum members. Registered subscriber as eagerly-initialized singleton in DI container. AuditService now accepts an explicit database_url parameter so it shares the same database as the rest of the application. All EventBus.emit() call sites are wrapped in try/except guards with structured logging, and ReactiveEventBus isolates per-handler failures so one failing subscriber cannot block others. server connect now emits per-setting CONFIG_CHANGED audit events via set_value(). SessionService.delete() emits ENTITY_DELETED. Exception messages in the DI container bootstrap are redacted before logging. CorrectionService is registered as a singleton in the DI container. Includes 23 Behave BDD scenarios, 5 Robot Framework integration tests, and ASV benchmarks. (#581)

Added

• Resource type single-inheritance via inherits field (ADR-042) (#513)
• Inheritance chain resolution, field merging, and polymorphic type matching
• ToolRegistry.find_tools_for_resource() for polymorphic tool binding
• Polymorphic handler resolution with ancestor-type fallback
• CLI: agents resource type list shows Inherits column; type show displays inheritance chain
• Alembic migration m6_004_resource_type_inherits adds inherits column to resource_types
• Fixed agents actor list raising a validation error on fresh projects. ActorRegistry._actor_name() built names via f"{provider}/{model}", which produced names with 2+ slashes when providers had models containing / (e.g. OpenRouter's anthropic/claude-sonnet-4-20250514). Now sanitises both provider and model names by replacing / with - and lowercasing to satisfy the spec pattern. Note: provider/model names are now lowercased; existing mixed-case built-in actors will be superseded by lowercased versions on the next ensure_built_in_actors() call. Includes Behave BDD regression scenarios, Robot Framework integration smoke tests, and ASV benchmarks. (#592)
• Added TDD regression tests for agents session list DI container wiring error (bug #554). _get_session_service() calls container.db() but the Container class has no db provider, raising AttributeError. Includes 10 Behave BDD scenarios (@tdd_bug @tdd_bug_554 @tdd_expected_fail) covering empty list, empty-list format validation (JSON/YAML/plain), init-then-list lifecycle, post-create list, rich/JSON/plain/YAML output formats, and stderr error-path assertions. Robot Framework integration smoke tests and ASV service-layer benchmarks. Implements @tdd_expected_fail infrastructure (Behave after_scenario hook and Robot listener) and migrates 18 existing TDD scenarios from @tdd @bugNNN to @tdd_bug @tdd_bug_NNN convention. (#554)
• Added TDD regression tests for agents session create DI container wiring error (bug #570). _get_session_service() calls container.db() but the Container class has no db provider, raising AttributeError. Same root cause as #554. Includes 4 Behave BDD scenarios (@tdd_bug @tdd_bug_570 @tdd_expected_fail), Robot Framework integration smoke tests, and ASV service-layer benchmarks. Tests exercise the real DI path with _service = None and a file-based SQLite database. Also implements the @tdd_expected_fail inversion infrastructure: a Behave after_scenario hook in features/environment.py that flips pass/fail for @tdd_expected_fail scenarios, and a Robot Framework Listener API v3 plugin (robot/tdd_expected_fail_listener.py) with identical semantics. Migrates 18 existing TDD scenarios from the old @tdd @bugNNN convention to standardised @tdd_bug @tdd_bug_NNN tags. (#570)
• Fixed intermittent race condition in M4 validation integration tests when running under pabot. Root cause was three-pronged: shared SQLite DB URL, shared CLEVERAGENTS_HOME directory, and singleton leaks in chained CLI helper invocations. Introduced composable Setup Database Isolation keyword in common.resource, per-suite temp directories, and centralised reset_global_state() in robot/helpers_common.py. Added timeout=30s to all Run Process calls in m4_e2e_verification.robot. (#563)
• Fixed agents project show not finding a project immediately after creation. Extended the session.commit() fix from #589 to also cover update() and delete() in NamespacedProjectRepository, and updated the class docstring to reflect that all mutating methods now commit within their own session. Includes 3 Behave BDD regression scenarios, Robot Framework integration smoke tests, and ASV benchmarks. (#590)
• Fixed agents project create not persisting projects to the database. NamespacedProjectRepository.create() called session.flush() but never session.commit(), so projects were invisible to subsequent agents project list calls. Added session.commit() and a finally: session.close() guard. Includes 4 Behave BDD regression scenarios, Robot Framework integration smoke tests, and ASV benchmarks. (#589)
• Added TDD-style Behave BDD tests for the built-in git-checkout resource type bootstrap. Three scenarios: one failing TDD test reproducing bug #524 (no bootstrap called during init), and two regression tests verifying bootstrap_builtin_types() seeds correct data and agents resource add git-checkout succeeds. Includes Robot Framework regression tests. (Drive-by: corrected bug reference from #523 to #524.) (#553)
• Added TDD-style Behave BDD tests for the built-in fs-directory resource type bootstrap. Three scenarios: one failing TDD test reproducing bug #524 (no bootstrap called during init), and two regression tests verifying bootstrap_builtin_types() seeds correct data and agents resource add fs-directory succeeds. Includes Robot Framework regression tests. (#537)
• Added TDD-style failing Behave BDD tests for the missing agents init --yes flag. Five scenarios: four TDD-failing tests (exit code, prompt suppression, -y alias, output summary) and one regression guard for interactive mode. Includes Robot Framework smoke tests and ASV benchmarks. Tests are intentionally failing until the bug fix for #522 is applied. (#536)
• Added Temporal Data Model (Revision-Aware RDF) with 3 storage tiers for the ACMS. Temporal metadata fields (valid_from, valid_until, is_current, is_revision_of) on UKO InformationUnit nodes enable revision chain tracking: when code changes, old nodes are marked historical and new revision nodes are created with back-links. Three storage tiers (hot/warm/cold) filter nodes by temporal scope (current/recent/all) with configurable retention (warm_retention_hours default 24h, cold_retention_days default 90d). Includes TemporalMetadata, TemporalNode, RevisionChain, TierQueryResult, TierRetentionConfig frozen domain models, TemporalBackend protocol, InMemoryTemporalBackend stub, TemporalService with structlog and DI, BackendSet.temporal typing upgrade from object | None to TemporalBackend | None. 99 Behave scenarios, 8 Robot Framework tests, ASV benchmarks, and reference documentation. (#577)
• Implemented UKO Layer 1 Domain Ontologies (uko-doc:, uko-data:, uko-infra:) in the OWL/Turtle ontology file (docs/ontology/uko.ttl). Added 17 uko-doc: classes (Document, Section, Paragraph, Citation, etc.), 13 uko-data: classes (Table, Column, ForeignKey, View, etc.), and 7 uko-infra: classes (Service, Endpoint, Port, etc.) with all spec-mandated properties and relationships. Updated all four DetailLevelMap presets (code_detail_map, docs_detail_map, database_detail_map, infra_detail_map) to be spec-complete with every named level. Added OntologyRegistry with domain lookup, Layer 1 listing, DetailLevelMap inheritance chain building, and Turtle syntax validation. Includes 31 Behave BDD scenarios and 6 Robot Framework integration tests. (#574)
• Added PostgreSQLAnalyzer and DockerComposeAnalyzer domain-specific analyzers (Phase 2 of issue #588). PostgreSQLAnalyzer parses DDL content via regex and extracts uko-data:Table, uko-data:Column, uko-data:ForeignKey, uko-data:View, and uko-data:Schema triples with column metadata (data type, nullability, primary key). DockerComposeAnalyzer parses Docker Compose YAML via yaml.safe_load and extracts uko-infra:DeploymentUnit, uko-infra:Service, uko-infra:Port, uko-infra:EnvironmentVariable, and uko-infra:connectsTo triples. Both satisfy AnalyzerProtocol and register in AnalyzerRegistry by file extension. Includes 34 Behave BDD scenarios covering all four analyzers (protocol conformance, registry operations, triple extraction, error handling, cross-analyzer URI scheme and confidence checks), 6 Robot Framework integration smoke tests, and updated __init__.py exports. (#588)
• Added TDD-style Behave BDD tests for the built-in git-checkout resource type bootstrap. Three scenarios: one failing TDD test reproducing bug #524 (no bootstrap called during init), and two regression tests verifying bootstrap_builtin_types() seeds correct data and agents resource add git-checkout succeeds. Includes Robot Framework regression tests. (#553)
• Added UKO Indexer for real-time index synchronization. UKOIndexer orchestrates analysis of resources into UKO triples via pluggable AnalyzerRegistry and simultaneously indexes into text, vector, and graph backends. Provenance metadata (ProvenanceMetadata, ProvenancedTriple) is attached to every triple, tracking source resource, file path, and temporal validity. Write-side index backend protocols (TextIndexBackend, VectorIndexBackend, GraphIndexBackend) are distinct from the existing read-side query protocols. Graceful degradation: if text or vector backends are None, the corresponding indexing step is silently skipped. Index lifecycle: index_resource (add), remove_resource (cleanup), reindex_resource (change). ContentReader protocol decouples the indexer from filesystem I/O. IndexLifecycleHook provides callbacks for indexing events. In-memory stub implementations for all three backends. ResourceFileWatcher monitors filesystem paths via watchdog and triggers re-indexing callbacks on file changes with configurable debouncing and optional RESOURCE_MODIFIED EventBus emission. Includes 166 Behave BDD scenarios, 9 Robot Framework integration tests, ASV benchmarks, and reference documentation. (#578)
• Added built-in virtual core resource types (file, directory, commit, branch, tag, tree) under examples/resource-types/. All use resource_kind: virtual, sandbox_strategy: none, user_addable: false. Equivalence metadata defines identity criteria per type (content hash for files, git object identity for commits/branches/tags/trees). Extended bootstrap registration in ResourceRegistryService to include virtual types and updated ResourceTypeSpec.BUILTIN_NAMES. Added reference documentation in docs/reference/resource_types_builtin.md. Includes Behave BDD tests, Robot integration tests, and ASV benchmarks. (#329)
• Added general-purpose domain event system under cleveragents.infrastructure.events. EventType StrEnum defines 38 typed event identifiers across 9 domains (plan lifecycle, decision, invariant, actor, tool, resource, sandbox, context, validation, session, budget). DomainEvent is a frozen Pydantic model with event_type, auto-UTC timestamp, auto-ULID correlation_id, plan_id, root_plan_id, session_id, actor_name, project_name, and details fields. EventBus is a @runtime_checkable Protocol with emit() and subscribe() methods. ReactiveEventBus is an RxPY Subject-backed in-process bus that dispatches synchronously to type-filtered handlers and exposes a raw rx.Observable stream for advanced operators. LoggingEventBus is a structlog-based bus for audit logging that requires no RxPY dependency. DecisionService and PlanLifecycleService accept an optional event_bus parameter (backward-compatible) and emit DECISION_CREATED, PLAN_CREATED, and PLAN_PHASE_CHANGED on significant state changes. ReactiveEventBus is registered as a Singleton in the DI container and wired into both services automatically. Includes Behave BDD unit tests (27 scenarios, 75 steps, 100% coverage on all new source files), Robot Framework smoke tests (9 cases), ASV performance benchmarks (5 suites), and reference documentation (docs/reference/event_bus.md). (#473)
• Validated M4 acceptance criteria for v3.3.0 milestone closure. All M4 E2E verification tests and correction/subplan smoke tests pass against the final v3.3.0 implementation. Added CLI-exercising integration tests for plan use, plan execute, and plan tree commands to verify the milestone success criteria through actual Typer CLI invocations. Split 1074-line helper into six focused modules (_common, _domain, _merge, _cli, _cli_errors, dispatcher) under the 500-line limit. Added CLI error-path tests for read-only plan execute, unavailable action, missing changeset, and empty decision tree. Extracted _make_subplan_status factory, _assert_exit_code and _assert_mock_called_once* wrappers, frozen timestamp constant, and shutil.which git pre-check. Removed tautological domain assertions in plan_tree and parallel_max. Fixed CONTRIBUTORS.md alphabetical ordering. (#495)
• Added minimal LSP server stub with agents lsp serve CLI command supporting the initialize, shutdown, and exit lifecycle handshake over JSON-RPC stdin/stdout transport with Content-Length header framing. Unsupported methods return MethodNotFound (-32601); requests before initialize return ServerNotInitialized (-32002); requests after shutdown return InvalidRequest (-32600). Transport hardening includes 10 MB max content-length, 32 max header lines, graceful recovery from malformed messages, and recursion-depth protection. LspServer stores an A2aLocalFacade for future server-mode wiring. --log-level flag controls logging verbosity. Includes 48 Behave BDD scenarios, Robot Framework smoke tests, ASV startup latency benchmarks, and docs/reference/lsp_stub.md. (#203)
• Validated M3 acceptance criteria for v3.2.0 milestone closure. All 10 E2E verification tests pass against the final implementation, exercising real CLI command paths (plan use, plan execute, plan tree, plan explain, project-scoped invariant add/list, dry-run and live plan correct), database-backed persistence, context snapshots, and invariant enforcement during strategize. Added acceptance criteria tags and milestone documentation to the robot suite. (#494)
• Added scoped backend view filtering for project-resource isolation in ACMS. ResourceScope holds the resolved set of resource ULIDs and project names visible to a plan (immutable, with include_paths/exclude_paths glob filtering via PurePath.full_match()). ScopedBackendView wraps text/vector/graph backends to auto-inject the scope parameter into every query, and filters TieredFragment visibility by project name and resource ID. ScopedBackendSet bundles scoped views for all three backend types. ResourceAliasResolver translates user-facing aliases to canonical resource ULIDs with uniqueness validation. resolve_resource_scope() builds a ResourceScope from projects with allowlist/denylist filtering. validate_project_scope() and validate_resource_scope() guard against out-of-scope access. Three enforcement hooks added to ContextTierService: get_scoped_by_resource, validate_fragment_scope, store_with_scope_check. Includes 74 Behave BDD scenarios (with full coverage-gap tests), 8 Robot Framework integration tests, ASV benchmarks, and reference documentation. (#193)
• Added builtin/plan-subplan tool for strategy actors to emit SUBPLAN_SPAWN or SUBPLAN_PARALLEL_SPAWN decisions. Validates payload via SubplanPayload (Pydantic), applies defaults (merge strategy, max_parallel, dependencies), generates rationale text, and optionally persists the Decision via an injected DecisionService. Includes register_subplan_tool, make_plan_subplan_spec factory, Behave unit tests, Robot Framework integration smoke tests, ASV benchmarks, and an actor YAML example. (#198)
• Extended CorrectionService._compute_affected_subtree() to BFS over both the structural decision tree (parent-child) and the influence DAG (decision_dependencies edges). Added cycle detection guard via visited set. Updated DecisionService.record_decision() to accept dependency_decision_ids parameter for recording influence relationships during decision creation. Added DecisionService.get_influence_edges() to retrieve influence DAG as adjacency list. All public methods on CorrectionService (analyze_impact, execute_revert, execute_correction, generate_dry_run_report) now accept optional influence_edges parameter. Includes Behave BDD scenarios, Robot Framework integration tests, and ASV benchmarks. (#542)
• Added Semantic Escalation system with AutonomyController class implementing should_proceed_automatically() that computes confidence scores from weighted factors (past_success_rate, codebase_familiarity, risk_assessment, invariant_complexity) and compares them against automation profile thresholds. Includes EscalationDecision, ConfidenceFactors, OperationContext, and HistoricalOutcome domain models. Historical success tracking records outcomes for future confidence computation. Integrates with all 8 built-in automation profiles. DI-wired as singleton autonomy_controller. Includes 48 Behave BDD scenarios, 10 Robot Framework integration tests, and ASV benchmarks. (#546)
• Added context strategy registry with ContextStrategy protocol, StrategyCapabilities, BackendSet, PlanContext, StrategyConfig, ContextStrategyResult, and StrategyRegistryEntry domain models. Six built-in stub strategies (simple-keyword, semantic-embedding, breadth-depth-navigator, arce, temporal-archaeology, plan-decision-context) with spec-mandated quality scores and backend requirements. StrategyRegistry supports config-driven registration, per-strategy timeout/max-fragment limits, per-project enable/disable overrides, plugin discovery from "module:ClassName" strings, and validation that strategies declare supported resource types. (#191)
• Fixed context inspect to display project-scoped tier fragment counts instead of global counts. Added ContextTierService.get_scoped_metrics() which returns fragment population counts filtered to the target project while keeping hit/miss counters as global service metrics. (#499)
• Fixed context simulate --focus to filter fragments by the specified focus URIs during dry-run assembly. Previously, focus URIs were passed to ContextRequest but not applied to fragment selection, making --focus a no-op. (#499)
• Wired project context CLI stubs (inspect, simulate, set, show) to live ACMS pipeline services. context inspect queries ContextTierService for tier metrics and per-project fragments with optional filtering by strategy, focus area, breadth, and depth. context simulate performs dry-run context assembly using CRP models with configurable token budget and assembly strategies. context set gains 12 ACMS pipeline options (hot_max_tokens, warm_max_decisions, cold_max_decisions, summary_max_tokens, temporal_scope, auto_refresh, focus_area, breadth, depth, assembly_strategy, retrieval_strategy, summary_strategy). context show displays ACMS pipeline configuration alongside context policy. Includes 28 Behave BDD scenarios for wiring coverage, updated Robot Framework integration tests, and reference documentation. (#499)
• Added async command execution infrastructure allowing plan phases (Execute, Apply) to run as background jobs processed by a thread pool of workers. AsyncJob Pydantic v2 domain model with ULID primary key, status state machine (queued -> running -> succeeded/failed/cancelled), and payload schema versioning. AsyncWorker service with ThreadPoolExecutor-backed concurrent execution, race-safe cancellation contract, stuck job detection, and job cleanup. InMemoryJobStore with atomic snapshot_counts() and single-pass remove_expired(). Plan lifecycle service wired to enqueue jobs when async.enabled is True. Error messages redacted via shared/redaction.py before persisting to the audit trail. Configurable via async.enabled, async.max_workers, async.poll_interval, async.job_timeout, async.job_ttl. Includes AsyncJobModel SQLAlchemy model, Alembic migration, Behave BDD scenarios, Robot Framework integration tests, ASV benchmarks, and docs/reference/async_architecture.md. (#312)
• Added hot/warm/cold context tiers with ContextTier, ActorRole, TieredFragment, TierBudget, ActorContextView, TierMetrics, and ScopedBackendView models. ContextTierService provides store/get, promotion/demotion with cold-tier summarisation hook, LRU eviction, per-actor filtered views (strategist/executor/reviewer), and project-scoped isolation. Settings: context_max_tokens_hot, context_max_decisions_warm, context_max_decisions_cold. DI-wired as singleton context_tier_service. Includes Behave BDD scenarios, Robot Framework integration tests, ASV benchmarks, and docs/reference/context_tiers.md. (#208)
• Added ExecutionEnvironment enum (host, container) and execution environment routing with priority chain (tool > plan > project > default). Includes ExecutionEnvironmentResolver service, --execution-environment CLI flags on agents plan use and agents plan execute, project-level context config support via agents project context set --execution-environment, tool runner wiring with container availability validation, and clear error when container is selected but no container resource is linked. Covered by Behave BDD scenarios, Robot Framework smoke tests, and ASV benchmarks. (#512)
• Added multi-project subplan support with MultiProjectMetadata, ProjectScope, ChangeSetSummary, CrossProjectDependency, and ProjectScopeResolver domain models. MultiProjectService provides scope initialization, context resolution, per-project changeset recording, and cross-project constraint validation. Plan model extended with multi_project_metadata field, is_multi_project property, and get_project_scope() method. CLI plan status shows per-project changeset summaries for multi-project plans. Includes Behave BDD scenarios, Robot Framework smoke tests, ASV benchmarks, and reference documentation. (#199)
• Added large-project hierarchical decomposition with 4+ levels and bounded context per subplan. Includes clustering heuristics (directory, language, size), bounded dependency closure with memoization for 10K+ files, DAG execution ordering with cycle detection, and DecisionService integration for strategy_choice + subplan_spawn recording. Configurable via planner_max_depth, planner_max_files_per_subplan, planner_max_tokens_per_subplan, planner_min_files_per_subplan settings. (#205)
• Added LLMTrace Pydantic v2 domain model and llm_traces database table with LLMTraceRepository for persisting LLM call telemetry (tokens, cost, latency, tool calls, context hash, streaming flag, retry count, error). Defined 14 OperationalMetricKey values with MetricEntry / MetricCollector for plan-level metrics. TraceService provides recording, querying, metric computation, and optional LangSmith forwarding when LANGCHAIN_TRACING_V2=true. (#500)
• Added SafetyProfile domain model with configurable safety constraints (allowed skill categories, sandbox/checkpoint requirements, human-approval flag, cost/retry limits) and integrated it into the Action model via from_config/as_cli_dict. Persistence backed by safety_profile_json column on LifecycleActionModel with Alembic migration c4_001_safety_profile_column. Includes resolve_safety_profile() stub that raises NotImplementedError in local mode (real enforcement deferred to server mode). Covered by 26 Behave BDD scenarios, 6 Robot Framework smoke tests, 5 ASV benchmark suites, and docs/reference/safety_profile.md reference documentation. (#332)
• Added devcontainer-instance, devcontainer-file, and container-instance built-in resource types with DevcontainerHandler and auto-discovery logic that scans for .devcontainer/ directories when git-checkout or fs-directory resources are linked. Includes CLI support, Behave/Robot/ASV tests, and reference documentation. (#511)
• Added full lifecycle management for devcontainer-instance resources: lazy activation on first tool target via DevcontainerHandler.resolve(), health checking with periodic liveness probes, manual agents resource stop/agents resource rebuild CLI commands (rebuild passes --reset-container to force container recreation), and automatic session-scoped cleanup on session close or plan completion. Lifecycle state tracked via ContainerLifecycleTracker with six states (detected/building/running/stopping/ stopped/failed) and validated transitions. Includes Behave BDD scenarios, Robot Framework integration tests, ASV benchmarks, and reference documentation. (#514)
• Added skeleton compressor service (SkeletonCompressorService) for ACMS context inheritance. Compresses parent plan context fragments by skeleton_ratio (0.0–1.0) for propagation to child plans. Persists SkeletonMetadata (ratio, token counts, source decision IDs) on the plan model for auditability. Includes stable fragment ordering, ratio validation with default handling, and compression summary. (#194)
• Wired A2A local facade handlers to live application services. session.create/close delegate to SessionService; plan.create/execute/status/diff/apply delegate to PlanLifecycleService; registry.list_tools and registry.list_resources delegate to ToolRegistry and ResourceRegistryService; event.subscribe delegates to A2aEventQueue. context.get returns a stub pending ACMS pipeline. Added domain-to-A2A error code mapping (NOT_FOUND, VALIDATION_ERROR, INVALID_STATE, PLAN_ERROR, etc.) via map_domain_error(). (#501)
• Added plan explain and plan tree CLI commands for decision tree inspection with json/yaml/table/rich output formats, and flags for superseded decisions, context snapshots, and reasoning details. (#174)
• Replaced behave-parallel subprocess-per-feature execution model (342 Python interpreter startups) with in-process execution via behave's Runner API. Sequential mode runs all features in a single Runner.run() call; parallel mode uses multiprocessing.Pool with fork for COW sharing of heavy modules. Coverage pipeline simplified to a single slipcover invocation wrapping the entire process. Unit tests: 24m21s -> 2m05s (91% reduction); coverage report: 75m20s -> 3m00s (96% reduction). (#481)
• Optimized 20 medium-slow BDD features (10-100s tier). Capped time.sleep and asyncio.sleep globally at 10ms in before_all to eliminate retry/backoff waits; originals saved as time._original_sleep / asyncio._original_sleep for timing-sensitive tests. Replaced subprocess.run CLI invocations with CliRunner in coverage step files. Switched persistence features to in-memory SQLite by default. Total tier runtime reduced from 565s to 21s (96%). (#480)
• Optimized the 8 slowest BDD feature files (100-248s each, 64% of total runtime). Added @mock_only tag support to skip unnecessary DB setup, extracted shared service-setup helpers in services_coverage_steps.py (~200 lines of duplicated boilerplate removed), and introduced lightweight in-memory plan service for actor-resolution tests. (#479)
• Added pre-migrated SQLite template database via scripts/create_template_db.py to eliminate repeated Alembic migrations per BDD scenario. Nox sessions propagate the template via CLEVERAGENTS_TEMPLATE_DB env var; features/environment.py monkey-patches MigrationRunner.init_or_upgrade to copy the template for fresh scenario temp DBs, falling through to real migrations for :memory:, existing files, and migration-runner unit tests. (#483)
• Replaced coverage.py (sys.settrace) with slipcover (bytecode instrumentation) for faster coverage collection. Each behave-parallel worker now produces per-feature JSON coverage files; slipcover --merge combines them. CI workflow JSON key lookups handle both slipcover and coverage.py output formats. Documentation updated to reflect slipcover as the coverage tool. (#482)
• Added checkpointing and rollback with CheckpointService for creating, listing, pruning, and deleting sandbox snapshots, and restoring sandbox state via plan rollback <plan_id> <checkpoint_id> CLI command. Checkpoint domain models (Checkpoint, CheckpointMetadata, CheckpointRetentionPolicy, RollbackResult) store sandbox refs, decision alignment, checkpoint type (pre_write, post_step, manual), filesystem path, size, and structured audit metadata (reason, source tool, phase). Retention policy auto-prunes oldest interior checkpoints when exceeding max_checkpoints (default 50), preserving the first and most recent. Guards reject rollback when plan is applied or sandbox is missing. CorrectionService accepts an optional CheckpointService integration point for future revert delegation. CheckpointRepository and CheckpointModel back persistence via the session-factory pattern (ADR-007), with UnitOfWorkContext.checkpoints for cross-repository atomicity. Alembic migration m6_001_checkpoint_metadata adds the checkpoint_metadata table. Includes Behave BDD scenarios (33 scenarios, 129 steps), Robot Framework integration tests (11 test cases), ASV benchmarks, and docs/reference/checkpointing.md. (#206)
• Added semantic validation service with AST-based rules for syntax errors, missing imports, broken references, duplicate imports, API misuse, and missing symbols. Includes rule registry, file-hash LRU cache, severity mapping, and ValidationPipeline integration. (#448)
• Added comprehensive M6 autonomy acceptance test suite covering A2A local facade dispatch (session/plan/registry/context/event operations), event queue pub/sub with local callbacks and close semantics, HTTP transport stub rejection, version negotiation, automation profile built-ins (8 profiles), custom profile creation/validation/YAML loading, guard enforcement (denylist, allowlist, call-limit, cost-budget, write-approval, apply-approval), and profile service 4-level resolution precedence. Includes Behave BDD scenarios (52), Robot Framework integration tests (11), ASV performance benchmarks (5 suites), JSON fixtures, and documentation update. (#211)
• Added MCP refresh hooks to wire notifications/tools/list_changed events from MCP servers to SkillRegistry. Introduced SkillRegistry.refresh(name) and refresh_all() to recompute flattened tool sets on demand. Added MCPRefreshHook with configurable debounce window (default 0.5 s) to coalesce rapid notification bursts into a single refresh call. Refresh skips tool-ref validation when no ToolRegistry is configured and emits a single WARNING with recovery steps. Results are summarised as an immutable SkillRefreshResult (refreshed / failed / skipped counts) for CLI and log output. Includes Behave unit tests (19 scenarios), Robot Framework integration tests (10 tests), ASV benchmarks, and docs/reference/skill_refresh.md. (#168)
• Added agents skill refresh <name>|--all command to recompute tool flattening and sync MCP-backed skills. Enhanced skill list, skill show, and skill tools outputs with capability summary fields, tool counts, and description columns. Added --format json/yaml schemas for refresh output. Updated CLI reference documentation with refresh examples and caching behavior. (#167)
• Added UKO Layer 0-3 ontology scaffolding (RDF/TTL) aligned with specification Section 14. Layer 0 (uko:) defines InformationUnit, Container, Atom, Annotation, Boundary plus contains/references/dependsOn relationships, content properties (hasRendering, renderingDepth, hasFullContent), provenance properties (sourceResource, sourcePath, sourceRange), and temporal properties (validFrom, validUntil, isCurrent, isRevisionOf). Layer 1 (uko-code:) defines Module, Callable, TypeDefinition, TestCase, Import plus hasReturnType/hasParameters/testsCallable. Layer 2 (uko-oo:) defines Class, Interface, Method, Attribute plus inheritsFrom/implements with rdfs:subPropertyOf. Layer 3 is reserved for DetailLevelMap insertions. Loader supports semantic domain prefixes, hyphenated prefix names, full-URI layer detection, multi-parent rdfs:subClassOf (DAG traversal via BFS), rdfs:domain/rdfs:range/rdfs:subPropertyOf resolution, and non-existent parent validation. (#189)
• Added ACMS v1 context assembly pipeline with UKO and CRP integration, three fusion strategies (relevance, recency, tiered), budget-constrained assembly, and extensible strategy registration. (#188)
• Added AgentSkillSpec loader that parses SKILL.md frontmatter and progressive disclosure sections into structured SkillStep objects with stable 1-based ordering. Supports namespaced naming (namespace/short_name), optional steps, version, compatibility, metadata, and allowed-tools frontmatter fields. Explicit validation raises actionable errors for missing name/description and invalid namespace format. Agent Skills are mapped to AgentSkillToolDescriptor with source="agent_skill" and read-only defaults. Support directories (scripts/, references/, assets/) are discovered automatically and exposed as read-only AgentSkillResourceSlot bindings. Includes docs/reference/agent_skills.md, Behave unit tests, Robot Framework integration tests, and ASV benchmarks. (#160)
• Added MCP adapter runtime (MCPToolAdapter) to connect to external MCP servers via stdio, SSE, and streamable-http transports. Supports full connection lifecycle (connect with timeout, reconnect, disconnect), tool discovery, input-validated invocation, and bulk registration into ToolRegistry with source="mcp" and checkpointable=False. Includes Behave unit tests, Robot integration test, ASV benchmarks, and docs/reference/mcp_adapter.md.

fix(permissions): address code-review findings for permission system (#448)

• Added input validation to check_permission() and get_role_bindings(): empty or whitespace-only principal and scope_id arguments now raise ValueError after stripping, preventing silent lookup misses.
• Aligned module docstring and reference docs to clarify that the enforce_permission decorator is available but not yet wired into CLI or service call sites — integration is deferred to a future pass.
• Added permissions.md to the docs nav in gen_ref_pages.py.
• Added Behave BDD scenarios covering empty, whitespace-only, and leading/trailing-whitespace inputs for both check_permission() and get_role_bindings().

feat(actor): extend hierarchical actor YAML schema and loader

• Extended actor YAML schema with hierarchical graph support: per-node LSP bindings (lsp_binding), tool-source references (tool_sources), and subgraph actor_ref.
• Added graph reachability validation — all nodes must be reachable from entry_node via edges or conditional routing targets.
• Improved loader error reporting with YAML line/column positions and Pydantic field-path hints.
• Added docs/reference/actor_config.md — practical configuration reference with hierarchical examples and error cases.
• Fixed examples/actors/graph_workflow.yaml to use actor_ref instead of deprecated actor_path.
• Added Robot smoke test for loading hierarchical actor YAML via ActorLoader.discover() (#157).
• Added decision persistence layer with DecisionRepository, DecisionModel, Alembic migration, tree queries (BFS traversal, path-to-root), superseded lookup, and ordered decision path retrieval. Includes Behave BDD scenarios, Robot Framework integration tests, and ASV benchmarks. (#171)
• Added token/cost tracking, budget enforcement (per-plan and per-day), provider fallback selection with capability filtering, and cost metadata for plan execution. New config keys budget_per_plan, budget_per_day, and fallback_providers control spending limits and provider ordering. Budget warnings are emitted at 90% usage, and requests are blocked at 100%. Per-provider cost table includes default token cost estimates for offline reporting. Budget exhaustion events are persisted in plan metadata for auditability. (#324)
• Added comprehensive Behave, Robot Framework, and ASV test coverage for CLI extension features including automation profile resolution, invariant ordering, actor override error cases, and output format snapshot assertions.
• Added comprehensive E2E test suite for M2 (Actor Graphs + Tool Sources) epic covering actor YAML loading, skill registry, tool lifecycle, and MCP stub tool discovery with Behave BDD scenarios, Robot Framework integration tests, and ASV performance benchmarks.
• Added plan-level and project-level advisory locking with configurable timeouts, re-entrant acquisition, conflict detection, lock renewal, graceful shutdown release, startup cleanup of expired locks, and diagnostics check for stale lock reporting. (#327)
• Added core plan apply service with diff review output (plain, rich, JSON, YAML), artifact summaries, apply summary persistence, merge-failure handling with sandbox rollback, and empty ChangeSet guard. (#155)
• Added validation pipeline with rule-based checks, severity levels (required vs informational), result aggregation, deterministic execution ordering, per-validation timeouts, and gate enforcement that blocks apply when required validations fail. (#175)
• Added validation-gated apply pipeline that blocks the Apply phase when required Execute-phase validations have not passed, transitions plans to constrained state with actionable CLI hints, and runs validation attachments during apply. (#176)
• Added diff review artifact model with inline comments, approval status, per-resource grouping, before/after content hashes, and plan apply service integration for plan diff and plan status outputs. (#303)
• Added definition-of-done gating that evaluates DoD criteria before apply, blocks phase transitions when required conditions are unmet, and stores pass/fail reasoning in the plan validation summary. (#178)
• Added error recovery patterns (retry, fallback, skip, abort) with structured recovery hints in CLI error output, plan executor integration, and error recovery service for capturing error category, recovery action, and retry history. (#186)
• Hardened template rendering by replacing unsafe Jinja2 usage with a sandboxed renderer that denies attribute access, function calls, and filters, allowing only {var} substitution from a fixed allowlist with max template length and max output size enforcement. (#319)
• Enforced explicit exception handling by introducing a CleverAgentsError base class with structured error types for configuration, provider, and file I/O failures, error code mapping, bare-except prohibition, and secret redaction in error details. (#320)
• Added 32 BDD scenarios to boost unit test coverage from 97.0% to 97.2%.
• Added Behave BDD scenarios for six under-tested modules (container, correction service, plan lifecycle service, plan CLI, skill CLI, database models) to exercise uncovered lines, exception-handling paths, and partial branches. (#446)
• Fixed failing Robot Framework integration tests related to security secrets handling.
• Fixed style check violations across the codebase.
• Fixed failing unit tests.
• Added changeset persistence and diff artifact storage for tracking multi-file changes across plan execution phases. (#163)
• Added AsyncResourceTracker for unified async resource lifecycle with timeout-bounded cleanup, leak detection via finalizer, and async context manager support.
• Enhanced LangGraphBridge with graceful task cancellation that awaits in-flight tasks.
• Added StateManager.close() and A2aEventQueue.close() for proper resource disposal.
• Tightened read-only enforcement: write-capable tools are now blocked on read-only plans regardless of the tool's own read_only flag.
• Added ReadOnlyViolationError to ChangeSetCapture to prevent write artifacts on read-only plans.
• Added CLI fail-fast guards on plan execute and plan apply for read-only plans.
• Added DecisionService with record/list/tree helpers and SnapshotStore for hash-based deduplication of context snapshots during plan execution.
• Expanded CONTRIBUTING.md with detailed guidance on the issue creation process, label system, ticket lifecycle, pull request requirements, and review/merge process.
• Added commit scope, quality, and message format guidelines to CONTRIBUTING.md.
• Migrated implementation timeline from the monolithic implementation plan to docs/timeline.md.
• Migrated implementation notes to docs/implementation-notes.md.
• Relocated remaining implementation plan content to the specification and CONTRIBUTING.md, and removed implementation_plan.md from the repository.
• Updated CONTRIBUTING.md to include project-specific conventions for tooling, testing, type checking, and code style.

v1.0.0

First release.