freemo d3cc7d30d7 fix(tool): persist tool registration to database after add ...

ToolRegistryRepository.create(), .update(), and .delete() called
session.flush() but never session.commit().  The CLI factory creates a
raw sessionmaker without a UnitOfWork wrapper, so the transaction was
never committed and SQLAlchemy performed an implicit rollback when the
session was garbage-collected.

The same bug existed in ValidationAttachmentRepository.attach() and
.detach().

Changes:
- Add session.commit() after session.flush() in all five mutating
  methods across ToolRegistryRepository and
  ValidationAttachmentRepository.
- Add finally: session.close() to guarantee session cleanup regardless
  of success or failure.
- Update class docstrings to reflect the new commit-on-write semantics.
- Add Behave BDD feature (tool_add_persist.feature) with scenarios for
  single-tool round-trip, multi-tool persistence, and duplicate
  rejection, using file-based SQLite to reproduce the cross-session
  issue.
- Add Robot Framework integration test (tool_add_persist.robot) with
  add-then-list and fresh-list-empty scenarios.
- Add ASV benchmark (tool_add_persist_bench.py) with
  track_list_after_add_count metric.

Key decisions:
- File-based SQLite (not in-memory) is used in tests because the bug
  only manifests when the session/engine is fully disposed between add
  and list, simulating separate CLI invocations.
- Step patterns are prefixed with "tool-persist" to avoid AmbiguousStep
  collisions with existing tool_registry_steps.py.
- The commit-in-repository approach was chosen over adding a UnitOfWork
  to the CLI factory because the CLI commands are simple CRUD operations
  that should auto-persist without requiring callers to remember to
  commit.

ISSUES CLOSED: #621

2026-03-08 22:11:49 +00:00

..

__init__.py

Significantly revamped the base project to use more robust static checking including benchmarks and integration test support

2025-10-31 16:18:53 -04:00

acms_backends_bench.py

feat(acms): add text, vector, and graph backend protocol implementations

2026-03-03 03:29:31 +00:00

acms_pipeline_bench.py

feat(acms): add ACMS v1 context pipeline

2026-03-05 01:28:50 +00:00

acms_pipeline_orchestrator_bench.py

feat(acms): implement pipeline orchestrator and Phase 1 components

2026-03-05 15:13:19 +00:00

acms_pipeline_phase2_bench.py

feat(acms): implement pipeline Phase 2 components

2026-03-05 10:27:36 -05:00

acms_pipeline_phase3_bench.py

feat(acms): implement pipeline Phase 3 components

2026-03-07 14:53:18 +00:00

acp_facade_bench.py

feat(M6.1): ACP facade stubs with transport, events, and versioning

2026-02-22 15:02:19 +00:00

action_cli_bench.py

feat(cli): align action commands to spec

2026-02-14 12:16:39 -05:00

action_schema_bench.py

docs(action): add action YAML schema and examples

2026-02-13 19:01:55 +05:30

actor_cli_bench.py

feat(cli): align actor commands to YAML

2026-02-24 19:12:01 +00:00

actor_compiler_bench.py

feat(actor): compile hierarchical actor configs to LangGraph

2026-02-24 17:57:18 +00:00

actor_examples_load_bench.py

test(actor): add ASV benchmarks for actor examples loading

2026-02-18 10:49:26 +00:00

actor_hierarchy_bench.py

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

2026-02-25 10:30:42 +00:00

actor_loading_bench.py

feat(actor): add actor registry and loader

2026-02-19 11:29:34 +00:00

actor_registry_bench.py

Fix: Fixed linting errors

2026-02-22 14:18:24 -05:00

actor_runtime_bench.py

Fix: Fixed linting errors

2026-02-22 14:18:24 -05:00

actor_schema_bench.py

perf(actor): add ASV benchmarks for actor schema

2026-02-17 13:54:27 +00:00

agent_skills_loader_bench.py

feat(skill): add agent skills loader

2026-02-26 09:10:35 +00:00

agent_skills_registry_bench.py

feat(concurrency): add plan and project locks

2026-02-25 10:48:05 -05:00

apply_pipeline_bench.py

feat(apply): add validation-gated apply pipeline

2026-02-25 10:01:57 +00:00

async_execution_bench.py

feat(async): add async command execution and workers

2026-03-04 23:47:20 +00:00

automation_legacy_cleanup_bench.py

refactor(automation): remove automation_level legacy fields

2026-02-20 15:57:21 +00:00

automation_profile_bench.py

feat(automation): add automation profiles and guards

2026-02-22 10:19:43 +00:00

automation_profile_cli_bench.py

feat(security): add safety profile model and enforcement stubs

2026-03-02 17:44:18 +00:00

automation_profile_resolution_bench.py

refactor(automation): remove automation_level legacy fields

2026-02-20 15:57:21 +00:00

autonomy_guardrails_bench.py

feat(automation): add autonomy guardrails and audit trail

2026-02-28 22:06:57 +00:00

bench_coverage_report.py

feat(context): add hot/warm/cold tiers and actor views

2026-03-03 17:01:57 +00:00

bench_subprocess_overhead.py

feat(context): add hot/warm/cold tiers and actor views

2026-03-03 17:01:57 +00:00

bench_unit_tests.py

feat(context): add hot/warm/cold tiers and actor views

2026-03-03 17:01:57 +00:00

binding_resolution_bench.py

Fix: Fixed linting errors

2026-02-22 14:18:24 -05:00

change_tracking_bench.py

feat(change): add ChangeSet models and invocation tracker

2026-02-21 16:27:40 +00:00

changeset_capture_bench.py

Merge branch 'master' into develop-20260217

2026-02-18 03:27:00 +00:00

changeset_persistence_bench.py

feat(changeset): persist changesets and diff artifacts

2026-02-26 02:47:14 +00:00

checkpoint_rollback_bench.py

feat(checkpoint): add checkpointing and rollback

2026-03-02 10:18:14 +00:00

ci_yaml_parse_bench.py

feat(ci): add nox-based PR validation workflow

2026-02-12 22:01:51 +00:00

cleanup_bench.py

Fix: Fixed linting errors

2026-02-22 14:18:24 -05:00

cli_benchmark.py

Tests: Added benchmarks for PlanGenerationGraph

2025-12-11 13:55:55 -05:00

cli_core_bench.py

feat(cli): enhance version/info/diagnostics with --format and --check

2026-02-18 12:18:03 +00:00

cli_extension_tests_bench.py

test(coverage): add Behave scenarios for remaining under-tested modules

2026-02-25 19:38:43 -05:00

cli_extensions_bench.py

test(cli): cover action and plan extensions

2026-02-24 20:11:42 +00:00

cli_format_bench.py

refactor(automation): remove automation_level legacy fields

2026-02-20 15:57:21 +00:00

cli_init_yes_bench.py

test(cli): add failing tests for agents init --yes missing option

2026-03-06 20:28:37 +00:00

cli_robot_flow_bench.py

fix(ci): remove stale AutomationLevel refs from benchmarks and prevent ANSI in JSON output

2026-02-20 21:46:46 +00:00

component_resolver_bench.py

feat(extensibility): implement pluggable scope chain resolution

2026-03-07 11:49:14 -05:00

concurrency_lock_bench.py

feat(concurrency): add plan and project locks

2026-02-25 10:48:05 -05:00

config_cli_bench.py

feat(config): add config service with multi-level resolution

2026-03-01 04:38:30 +00:00

config_project_scope_bench.py

feat(config): add project-scoped config overrides

2026-03-02 15:05:20 +00:00

config_resolution_bench.py

feat(config): add config service with multi-level resolution

2026-03-01 04:38:30 +00:00

context_fragment_models_bench.py

feat(acms): add ContextFragment and ScoredFragment data models

2026-03-05 14:11:23 +00:00

context_strategies_bench.py

feat(acms): implement context strategies batch 1

2026-03-05 12:58:57 +00:00

context_strategy_bench.py

feat(acms): add context strategy registry

2026-03-05 22:00:15 +00:00

context_tiers_bench.py

feat(context): add hot/warm/cold tiers and actor views

2026-03-03 17:01:57 +00:00

cost_controls_bench.py

feat(provider): add cost controls and fallback

2026-02-25 12:08:01 -05:00

coverage_report_bench.py

feat(repo): add resource repositories

2026-02-16 21:35:54 +00:00

cross_plan_correction_bench.py

feat(correction): implement cross-plan correction cascading with child plan state handling

2026-03-04 21:20:47 +00:00

crp_model_bench.py

feat(acms): add context request protocol models

2026-03-02 14:32:31 +00:00

db_migration_action_args_bench.py

feat(db): add spec-aligned action and plan tables with migrations, ORM models, and benchmarks

2026-02-13 13:05:20 -05:00

db_migration_actions_bench.py

feat(db): add spec-aligned action and plan tables with migrations, ORM models, and benchmarks

2026-02-13 13:05:20 -05:00

db_migration_plans_bench.py

refactor(automation): remove automation_level legacy fields

2026-02-20 15:57:21 +00:00

decision_correction_bench.py

feat(M4.2): Correction service with revert/append BFS + dry-run

2026-02-22 16:40:06 +00:00

decision_correction_model_bench.py

feat(correction): add correction model and CLI hooks

2026-02-22 11:07:35 +00:00

decision_di_bench.py

feat(context): add hot/warm/cold tiers and actor views

2026-03-03 17:01:57 +00:00

decision_model_bench.py

feat(decision): add decision domain and context snapshots

2026-02-23 22:19:19 +00:00

decision_persistence_bench.py

refactor(test): rename decision persistence files to avoid conflict with master

2026-02-26 16:13:44 +00:00

decision_persistence_serialization_bench.py

refactor(test): rename decision persistence files to avoid conflict with master

2026-02-26 16:13:44 +00:00

decision_recording_bench.py

feat(service): add decision recording and snapshot store

2026-03-03 12:18:27 +00:00

depth_breadth_projection_bench.py

feat(acms): implement depth/breadth projection system

2026-03-05 15:42:20 +00:00

devcontainer_handler_bench.py

feat(context): add hot/warm/cold tiers and actor views

2026-03-03 17:01:57 +00:00

diff_review_bench.py

feat(change): add diff review artifacts

2026-02-25 10:02:38 +00:00

docs_build_bench.py

style: fix formatting

2026-02-20 20:38:53 +00:00

dod_evaluation_bench.py

feat(dod): enforce definition-of-done gating

2026-02-25 10:04:31 +00:00

error_recovery_bench.py

feat(concurrency): add plan and project locks

2026-02-25 10:48:05 -05:00

event_bus_bench.py

feat(events): add EventBus protocol and ReactiveEventBus implementation

2026-03-02 11:54:53 +00:00

execution_environment_bench.py

feat(execution): add execution environment routing

2026-03-03 14:48:55 -05:00

file_tool_bench.py

feat(skill): add file operation skills

2026-02-21 10:18:26 -05:00

git_tool_bench.py

test(robot): fix failing integration tests related to safe.directory config and git version

2026-02-21 18:11:31 +00:00

influence_dag_bench.py

feat(decision): implement influence DAG traversal in correction affected subtree computation

2026-03-04 15:36:34 +00:00

inline_tool_bench.py

feat(skill): add inline tool executor

2026-02-20 08:50:08 -05:00

invariant_merge_bench.py

Fix: Fixed linting errors

2026-02-22 14:18:24 -05:00

invariant_reconciliation_bench.py

feat(actor): implement built-in invariant reconciliation actor

2026-03-04 20:26:42 +00:00

large_project_decompose_bench.py

feat(plan): add large-project decomposition and dependency closure

2026-03-03 21:44:20 +00:00

legacy_removal_bench.py

refactor(automation): remove automation_level legacy fields

2026-02-20 15:57:21 +00:00

llm_trace_bench.py

feat(observability): add LLMTrace model and operational metrics

2026-03-03 17:04:17 -05:00

lsp_registry_bench.py

feat(lsp): add registry and runtime stubs

2026-02-22 10:15:25 +00:00

lsp_stub_bench.py

feat(lsp): add LSP server stub

2026-03-06 18:16:47 +00:00

m1_sourcecode_smoke_bench.py

test(e2e): add M1 source-code plan lifecycle suite

2026-02-25 04:50:43 +00:00

m2_actor_tool_smoke_bench.py

test(coverage): add Behave scenarios for remaining under-tested modules

2026-02-25 19:38:43 -05:00

m3_smoke_bench.py

test(e2e): add M3 decision + validation suites

2026-02-25 21:26:19 +00:00

m4_smoke_bench.py

fix(test): correct mock targets, method names, ULIDs, and CLI args in M4 smoke suite

2026-02-26 02:01:47 +00:00

m5_smoke_bench.py

test(e2e): add M5 ACMS + context suites

2026-02-27 20:20:13 +00:00

m6_acceptance_bench.py

test(e2e): add M6 autonomy acceptance suite

2026-02-27 20:31:15 +00:00

mcp_runtime_bench.py

feat(skill): add MCP adapter for external tools

2026-02-25 13:17:26 +00:00

multi_project_bench.py

feat(plan): add multi-project subplan support

2026-03-03 14:55:58 -05:00

output_rendering_bench.py

feat(cli): add output rendering framework with materialization strategies

2026-02-21 10:19:45 -05:00

permission_check_bench.py

feat(context): add hot/warm/cold tiers and actor views

2026-03-03 17:01:57 +00:00

persistence_robot_bench.py

fix(ci): remove stale AutomationLevel refs from benchmarks and prevent ANSI in JSON output

2026-02-20 21:46:46 +00:00

persistence_suites_bench.py

refactor(automation): remove automation_level legacy fields

2026-02-20 15:57:21 +00:00

phase_reversion_bench.py

Fix: linting errors fixed

2026-02-23 09:47:00 -05:00

plan_actor_integration_bench.py

feat(plan): execute strategize and execute via actors

2026-02-21 10:18:26 -05:00

plan_cli_bench.py

refactor(automation): remove automation_level legacy fields

2026-02-20 15:57:21 +00:00

plan_cli_smoke_bench.py

refactor(automation): remove automation_level legacy fields

2026-02-20 15:57:21 +00:00

plan_diff_bench.py

Tests: Significantly improved coverage of the unit tests

2026-02-22 00:43:08 -05:00

plan_execute_bench.py

feat(M1.2): PlanExecutionContext, RuntimeExecuteActor, and runtime mode

2026-02-22 15:13:43 +00:00

plan_explain_bench.py

feat(cli): add plan explain and decision tree outputs

2026-03-03 12:10:25 +00:00

plan_generation_benchmark.py

fix(provider): remove FakeListLLM defaults

2026-02-27 09:47:10 -05:00

plan_lifecycle_persistence_bench.py

fix(tests): resolve unit test and benchmark failures

2026-02-17 02:24:35 +00:00

plan_model_bench.py

fix(tests): resolve unit test and benchmark failures

2026-02-17 02:24:35 +00:00

plan_phase_bench.py

Fix: Fixed linting errors

2026-02-22 14:18:24 -05:00

plan_phase_migration_bench.py

Merge branch 'master' into feature/q0-min-coverage

2026-02-17 02:35:20 +00:00

plan_repository_bench.py

refactor(automation): remove automation_level legacy fields

2026-02-20 15:57:21 +00:00

plan_resume_bench.py

feat(concurrency): add plan resume

2026-02-25 14:00:04 -05:00

project_cli_bench.py

feat(cli): add project commands (core)

2026-02-16 23:56:55 -05:00

project_context_cli_bench.py

Merge branch 'master' into develop-20260217

2026-02-18 03:27:00 +00:00

project_context_policy_bench.py

Merge branch 'master' into develop-20260217

2026-02-18 03:27:00 +00:00

project_migration_bench.py

Merge branch 'master' into feature/q0-min-coverage

2026-02-17 02:35:20 +00:00

project_repository_bench.py

Tests: Significantly improved coverage of the unit tests

2026-02-22 00:43:08 -05:00

provider_selection_bench.py

fix(provider): remove FakeListLLM defaults

2026-02-27 09:47:10 -05:00

repl_bench.py

feat(cli): add interactive repl

2026-02-23 03:11:12 +00:00

resource_cli_bench.py

feat(cli): add resource commands (core)

2026-02-16 16:46:54 -05:00

resource_cli_tree_bench.py

feat(cli): add resource tree and inspect commands

2026-02-20 08:48:33 -05:00

resource_dag_bench.py

Fix: Fixed linting errors

2026-02-22 14:18:24 -05:00

resource_handler_bench.py

feat(resource): add handler runtime for git-checkout and fs-directory

2026-02-23 22:20:44 +00:00

resource_registry_bench.py

refactor(benchmark): clean up resource registry bench per review

2026-02-23 22:20:44 +00:00

resource_registry_migration_bench.py

Merge branch 'master' into feature/q0-min-coverage

2026-02-17 02:35:20 +00:00

resource_repository_bench.py

feat(session): add session persistence and repositories

2026-02-18 00:10:15 +00:00

resource_service_bench.py

feat(cli): add resource commands (core)

2026-02-16 16:46:54 -05:00

resource_type_builtin_bench.py

feat(resource): add git-checkout and fs-directory resource types

2026-02-15 10:44:14 -05:00

resource_type_fs_bench.py

Merge branch 'master' into develop-20260217

2026-02-18 03:27:00 +00:00

resource_type_model_bench.py

feat(resource): add resource type model + schema loader

2026-02-15 15:19:09 +00:00

resource_type_schema_bench.py

feat(resource): add resource type model + schema loader

2026-02-15 15:19:09 +00:00

safety_profile_bench.py

feat(security): add safety profile enforcement

2026-03-03 22:21:14 +00:00

safety_profile_model_bench.py

feat(security): add safety profile model and enforcement stubs

2026-03-02 17:44:18 +00:00

sandbox_boundary_bench.py

feat(sandbox): implement sandbox boundary algebra and domain computation

2026-03-04 15:59:15 +00:00

sandbox_checkpoint_bench.py

feat(sandbox): add checkpoint and rollback hooks

2026-02-27 23:08:55 +00:00

scale_fixture_bench.py

test(perf): add scale test fixtures

2026-02-20 03:31:43 +00:00

scoped_view_bench.py

feat(acms): add scoped backend view filtering

2026-03-06 00:49:33 +00:00

search_tool_bench.py

feat(skill): add directory and search skills

2026-02-21 10:18:26 -05:00

security_async_cleanup_bench.py

fix(security): address PR #435 review feedback

2026-02-26 14:30:43 +00:00

security_audit_bench.py

Tests: Significantly improved coverage of the unit tests

2026-02-22 00:43:08 -05:00

security_eval_bench.py

fix(security): remove eval-based config parsing

2026-02-21 16:32:03 +00:00

security_exception_bench.py

fix(security): enforce explicit exception handling

2026-02-25 10:05:57 +00:00

security_readonly_bench.py

feat(security): enforce read-only actions

2026-02-26 20:33:20 +00:00

security_scan_bench.py

feat(qa): align security scans with nox

2026-02-13 19:24:24 +00:00

security_secrets_bench.py

feat(security): add secrets masking and validation (H-21/SEC5)

2026-02-19 11:15:18 +00:00

security_template_bench.py

fix(security): harden template rendering

2026-02-25 10:06:27 +00:00

semantic_escalation_bench.py

feat(autonomy): implement semantic escalation with confidence scoring and threshold comparison

2026-03-04 12:18:51 -05:00

semantic_validation_bench.py

feat(context): add hot/warm/cold tiers and actor views

2026-03-03 17:01:57 +00:00

semantic_validation_suite_bench.py

test(validation): add semantic validation suites

2026-03-02 22:05:53 +00:00

server_stub_bench.py

feat(context): add hot/warm/cold tiers and actor views

2026-03-03 17:01:57 +00:00

session_cli_bench.py

feat(cli): add session commands

2026-02-20 01:10:19 +00:00

session_model_bench.py

feat(session): add session domain models and contracts

2026-02-14 03:50:40 +00:00

session_persistence_bench.py

Fix: Fixed linting errors

2026-02-22 14:18:24 -05:00

skeleton_compressor_bench.py

refactor(acms): unify ContextFragment model hierarchies by extending CRP base types

2026-03-05 21:38:55 +00:00

skill_add_persist_bench.py

fix(skill): persist skill registration to database after add

2026-03-08 02:57:44 +00:00

skill_cli_bench.py

feat(cli): add skill tools and refresh commands

2026-02-26 10:57:07 +00:00

skill_context_bench.py

Fix: Fixed linting errors

2026-02-22 14:18:24 -05:00

skill_flatten_bench.py

feat(actor): compile hierarchical actor configs to LangGraph

2026-02-24 17:57:18 +00:00

skill_protocol_bench.py

feat(skill): add skill protocol and metadata

2026-02-20 08:50:08 -05:00

skill_refresh_bench.py

feat(skill): add MCP refresh hooks

2026-02-26 12:29:49 +00:00

skill_registry_bench.py

feat(skill): add skill registry persistence

2026-02-21 16:30:40 +00:00

skill_registry_persist_bench.py

feat(skill): persist flattened tool sets

2026-02-27 20:09:26 +00:00

skill_resolution_bench.py

feat(skill): add skill domain model and resolver

2026-02-14 03:54:14 +00:00

skill_schema_bench.py

style(skill): apply ruff auto-formatting to skill schema files

2026-02-17 10:13:19 +00:00

subplan_actor_tool_bench.py

feat(actor): add plan_subplan tool and decision emission

2026-02-27 08:02:48 +00:00

subplan_execution_bench.py

feat(context): add hot/warm/cold tiers and actor views

2026-03-03 17:01:57 +00:00

subplan_model_validation_bench.py

test(domain): add subplan model suites

2026-02-19 22:07:56 +00:00

subplan_spawn_bench.py

feat(service): add subplan service and spawn workflow

2026-03-02 09:41:25 -05:00

tool_add_persist_bench.py

fix(tool): persist tool registration to database after add

2026-03-08 22:11:49 +00:00

tool_builtin_file_bench.py

feat(repo): add resource repositories

2026-02-16 21:35:54 +00:00

tool_cli_bench.py

feat(cli): add tool and validation commands

2026-02-20 08:49:30 -05:00

tool_lifecycle_bench.py

feat(tool): add tool lifecycle runtime

2026-02-14 18:55:48 +00:00

tool_model_bench.py

Fix: Fixed linting errors

2026-02-22 14:18:24 -05:00

tool_registry_bench.py

feat(tool): add tool registry persistence

2026-02-17 20:28:20 +00:00

tool_router_bench.py

feat(change): add tool router for providers

2026-02-21 10:23:31 -05:00

tool_runtime_bench.py

Fix: Fixed linting errors

2026-02-22 14:18:24 -05:00

tool_wrapping_bench.py

feat(validation): implement tool wrapping runtime (wraps + transform delegation)

2026-03-04 18:21:19 +00:00

uko_analyzers_bench.py

feat(uko): add analyzer plugin framework and initial domain analyzers

2026-03-05 19:20:39 +00:00

uko_load_bench.py

feat(uko): add UKO ontology scaffolding

2026-03-04 22:40:34 +00:00

unified_context_models_bench.py

refactor(acms): unify ContextFragment model hierarchies by extending CRP base types

2026-03-05 21:38:55 +00:00

uow_lifecycle_bench.py

refactor(automation): remove automation_level legacy fields

2026-02-20 15:57:21 +00:00

validation_apply_bench.py

feat(apply): run validation attachments

2026-02-25 10:03:21 +00:00

validation_edge_bench.py

test(validation): add edge case suites

2026-02-20 02:54:08 +00:00

validation_pipeline_bench.py

feat(concurrency): add plan and project locks

2026-02-25 10:48:05 -05:00