Docs: Updated daily timeline documentation

docs/gen_ref_pages.py

@@ -149,7 +149,9 @@ nav[("di",)] = "di.md"
 nav[("mcp_adapter",)] = "mcp_adapter.md"
 nav[("read_only_actions",)] = "read_only_actions.md"
 nav[("sandbox",)] = "sandbox.md"
+nav[("semantic_validation",)] = "semantic_validation.md"
 nav[("skill_refresh",)] = "skill_refresh.md"
+nav[("subplans",)] = "subplans.md"
 
 # Write the literate-nav summary file for the Reference section
 with mkdocs_gen_files.open("reference/SUMMARY.md", "w") as nav_file:

docs/timeline.md

@@ -10,14 +10,14 @@ The following chart shows all 29 epics across 9 legendary workstreams, 7 milesto
 @startgantt
 
 title CleverAgents Core — Epic-Level Project Schedule
-footer Generated 2026-02-28 | 29 Epics | 9 Legendaries | 7 Milestones | 6 Developers | ~1500 SP
+footer Generated 2026-03-02 | 29 Epics | 9 Legendaries | 7 Milestones | 6 Developers | ~1500 SP
 
 Project starts 2026-02-03
 saturday are closed
 sunday are closed
 printscale weekly zoom 2
 
-today is 2026-02-28
+today is 2026-03-02
 today is colored in #FF6666
 
 <style>
@@ -428,7 +428,7 @@ saturday are closed
 sunday are closed
 printscale weekly zoom 2
 
-today is 2026-02-28
+today is 2026-03-02
 today is colored in #FF6666
 
 <style>
@@ -1948,15 +1948,15 @@ This section provides a high-level overview of the CleverAgents implementation r
 
 ### Current Status Summary
 
-As of Day 20 (2026-02-28), the project has **~347 closed milestone issues out of ~394 assigned milestone issues** across all milestones (~88% overall completion rate). A continued productivity surge over Days 18-20 closed **~20 additional issues** since the last update, completing the M1 and M2 critical paths entirely and advancing M4 security hardening.
+As of Day 22 (2026-03-02), the project has closed **~360 milestone issues out of ~410 assigned milestone issues** across all milestones (~88% overall completion rate). Days 20-22 closed **~15 additional issues**, completing M4's last blocking feature (subplan execute+merge), landing the config service, and dramatically improving test infrastructure performance.
 
-**Days 19-20 highlights**: FakeListLLM defaults removed (#459, Jeff) — M1 is now **fully closed**. MCP adapter merged (#434, Aditya). Agent skills loader merged (#453, Aditya). Skill CLI tools+refresh merged (#454, Aditya). MCP refresh hooks merged (#455, Aditya). Skill persistence with flattened tool sets merged (#460, Jeff). Decision service wiring merged (#461, Jeff). Security read-only actions (#436, Hamza). Async cleanup (#435, Hamza). Sandbox checkpoint/rollback hooks (#462, Jeff). M6 E2E suite merged (#457, Brent). Coverage improvements for 9 under-covered modules (#468). SafetyProfile spec composition docs (#471/#472).
+**Days 21-22 highlights**: Subplan execute+merge merged (#184, Luis — PR #444 → merged Mar 1). Config service with multi-level resolution merged (#258, Jeff — PR #474). Autonomy guardrails and audit trail merged (#204, Luis). Semantic validation service merged (#207, Luis). Permission system merged (Jeff). Test suite performance optimized by 90%+ (#479-#483, Jeff — PR #493): BDD suite 26min→2min, coverage report 75min→5min. Coverage improvements for 8 under-covered modules (#475). Devcontainer integration and resource type inheritance added to spec (#491).
 
-**M1 and M2 are now complete.** M3 has 2 remaining issues (#172 decision recording, #174 plan explain CLI). M4 has 1 remaining issue (#184 subplan execute, In Review with open PR #444). **The critical focus now shifts to M5 (ACMS/context)** which has 15 open issues and only 6 days to target.
+**M1 and M2 are fully complete. M3 has 2 remaining feature issues** (#172 decision recording, #174 plan explain CLI — both Hamza, PRs #433/#464 pending merge) plus E2E validation (#494). **M4 is feature-complete** — only E2E validation (#495) and the Security Epic (#362) remain open. **The critical path is now M5 (ACMS/context)** which has ~15 open feature issues with 4 days to target. M6 has 11 remaining feature issues (6 Luis PRs were merged or are in review).
 
-!!! warning "Schedule Risk: 4-6 Days Behind (Stable)"
+!!! warning "Schedule Risk: 3-4 Days Behind (Narrowing)"
 
-    The project is running **4-6 days behind** the original aggressive schedule, improved from 5-7 days at Day 18. M1 and M2 are now fully complete. M3 and M4 are nearly complete (2 and 1 remaining issues respectively). The bottleneck has shifted to **M5 (ACMS v1 + context scaling)** which has 15 open issues (all unassigned) with a 6-day runway to its Mar 6 target. M6 (autonomy hardening) has 13 open issues with 10 days to target. Rui returned from leave on Feb 27 and is now available for testing assignments.
+    The project is running **3-4 days behind** the original aggressive schedule, narrowed from 4-6 days at Day 20. M1 and M2 are fully complete. M3 is nearly complete (2 feature issues with PRs pending merge). **M4 is feature-complete** — subplan execution merged Mar 1. The bottleneck is now **M5 (ACMS v1 + context scaling)** which has ~15 open issues with only 4 days to its Mar 6 target — the ACMS pipeline, UKO ontology, CRP protocol, and context strategies are the critical path. M6 (autonomy hardening) has ~11 open issues with 8 days to target; autonomy guardrails, semantic validation, and permission system already landed. Rui is available for testing assignments since Feb 27.
 
 ### Parallel Workstreams
 
@@ -1964,14 +1964,14 @@ Development is organized into six concurrent workstreams plus continuous quality
 
 | Track | Focus Area | Status |
 | :---- | :--------- | :----- |
-| **A** — Plan Lifecycle | Action/plan domain models, persistence, CLI alignment, execute/apply wiring | **Complete.** Apply pipeline with validation gating merged (#155). Changeset persistence merged (#163). Concurrency locks + plan resume merged (#327, #328). Config service (#352) deferred to M5. Decision service wiring merged (#461). |
+| **A** — Plan Lifecycle | Action/plan domain models, persistence, CLI alignment, execute/apply wiring | **Complete.** Apply pipeline, changeset persistence, concurrency locks, plan resume, decision service wiring all done. Config service merged (#258, Mar 1). |
 | **B** — Projects & Resources | Resource registry, project model, resource types, sandbox strategies, CLI | **Complete.** Registry, models, CLI, handler runtime (git-checkout + fs-directory), DAG metadata all done. |
-| **C** — Actors, Tools, Skills | Actor YAML schema/loader/compiler, tool registry/runtime, skill framework, MCP adapter, validation runner | **Complete.** Actor compiler, agent skills discovery, actor CLI, skill registry flattening, validation pipeline all done. MCP adapter merged (#434). Agent skills loader merged (#453). Skill CLI merged (#454). MCP refresh hooks merged (#455). Skill persistence merged (#460). |
-| **D** — Decisions & Apply | Decision tree model, change tracking, diff review, apply pipeline, correction engine | **Nearly complete.** Decision persistence merged (#171). Validation-gated apply merged (#176). Decision service wiring merged (#461). Remaining: decision recording (#172), plan explain CLI (#174). Invariant enforcement (#173) closed. |
-| **E** — Subplans | Subplan domain model, orchestration, parallel execution, three-way merge | **Nearly complete.** Domain model done. Subplan execute+merge (#184) In Review with PR #444. |
-| **F** — ACMS & Context | UKO ontology, CRP protocol, context strategies, assembly pipeline, hot/warm/cold tiers | **In progress.** ACMS v1 context pipeline (#188) and UKO scaffolding (#189) are In Progress. 12 additional M5 issues remain unassigned. This is the new critical path. |
-| **Q** — Quality & CI | Pre-commit hooks, Forgejo CI/CD, coverage enforcement (97%), security scanning | **Complete.** Security read-only actions (#436) and async cleanup (#435) merged. Coverage improvements for 9 modules (#468) merged. Sandbox checkpoint hooks (#462) merged. |
-| **T** — Testing | Behave unit tests, Robot integration tests, ASV benchmarks, end-to-end smoke suites | **Strong progress.** M1-M4 E2E suites all merged. M6 E2E suite merged (#457). M5 E2E suite (#406) In Review. Rui returned Feb 27 and is available. |
+| **C** — Actors, Tools, Skills | Actor YAML schema/loader/compiler, tool registry/runtime, skill framework, MCP adapter, validation runner | **Complete.** All components merged including MCP adapter (#434), agent skills (#453), skill CLI (#454), MCP hooks (#455), skill persistence (#460). |
+| **D** — Decisions & Apply | Decision tree model, change tracking, diff review, apply pipeline, correction engine | **Nearly complete.** Decision persistence, validation-gated apply, decision service wiring all done. Remaining: decision recording (#172, PR #433) and plan explain CLI (#174, PR #464) — both Hamza, PRs pending merge. |
+| **E** — Subplans | Subplan domain model, orchestration, parallel execution, three-way merge | **Complete.** Subplan execute+merge (#184) merged Mar 1 via PR #444 (Luis). Domain model, orchestration, and merge strategies all operational. |
+| **F** — ACMS & Context | UKO ontology, CRP protocol, context strategies, assembly pipeline, hot/warm/cold tiers | **In progress — critical path.** UKO scaffolding (#189, PR #466) and ACMS pipeline (#188, PR #465) In Progress (Hamza). ~12 additional M5 issues remain. Config service landed (#258). |
+| **Q** — Quality & CI | Pre-commit hooks, Forgejo CI/CD, coverage enforcement (97%), security scanning | **Complete.** Test suite performance optimized 90%+ (#479-#483): BDD 26min→2min, coverage 75min→5min. Coverage at 98%. |
+| **T** — Testing | Behave unit tests, Robot integration tests, ASV benchmarks, end-to-end smoke suites | **Strong progress.** M1-M4 and M6 E2E suites all merged. M5 E2E merged (#469). Rui available since Feb 27. M3/M4/M5/M6 E2E validation issues (#494-#497) remain. |
 
 ### What Has Been Completed
 
@@ -2008,21 +2008,29 @@ The following major areas are fully or substantially implemented:
 - **Coverage improvements**: Behave BDD scenarios added for 9 under-covered modules (#468 merged 2026-02-27), improving overall test coverage.
 - **M6 E2E suite**: Firefox-scale autonomous porting verification suite merged (#457 merged 2026-02-27, Brent).
 - **SafetyProfile specification**: SafetyProfile recognized as composed sub-model of AutomationProfile in spec docs (#471/#472 merged 2026-02-28).
+- **Subplan execute and merge**: Subplan execution scheduler with sequential/parallel/dependency_ordered modes and merge strategies (git three-way, sequential apply, fail on conflict, last wins) merged (#184/PR #444 merged 2026-03-01, Luis). **M4 feature-complete.**
+- **Config service**: Multi-level configuration resolution with project-scoped overrides (#258/PR #474 merged 2026-03-01, Jeff).
+- **Autonomy guardrails**: Autonomy guardrails (max steps, tool budget, required confirmations) with audit trail persistence (#204 merged 2026-02-28, Luis).
+- **Semantic validation**: Semantic validation hooks during strategize/execute with syntax, import, and reference checks for Python (#207 merged 2026-02-28, Luis).
+- **Permission system**: Permission checks for resource access and tool invocation (merged 2026-03-01, Jeff).
+- **Test suite performance**: 90%+ reduction in test runtime (#479-#483/PR #493 merged 2026-03-02, Jeff): BDD unit tests 26min→2min (92%), coverage report 75min→5min (93%), coverage improved to 98%. Slipcover bytecode instrumentation replaces coverage.py, shared template DB eliminates per-scenario migration overhead, in-process parallelism replaces subprocess spawning.
+- **Coverage improvements (Day 21)**: Behave BDD tests for 8 under-covered modules (#475 merged 2026-03-01).
+- **Devcontainer integration**: Devcontainer resource type and resource type single inheritance added to specification (#491/PR #492 merged 2026-03-01).
 
 ### What Remains To Be Done
 
-The majority of the specification's domain models, services, CLI commands, and infrastructure modules are now implemented. M1 and M2 are fully complete. The following areas still require completion:
+The majority of the specification's domain models, services, CLI commands, and infrastructure modules are now implemented. M1, M2, and M4 are fully complete (feature-wise). M3 has 2 remaining feature PRs pending merge. The following areas still require completion:
 
-- **Decision recording service**: Wire decision recording into the strategize/execute phases so decisions are automatically captured during plan execution (#172, In Progress, branch exists).
-- **Plan explain CLI**: Plan tree and explain commands for decision tree visualization (#174, In Progress, branch exists).
-- **Subplan execute and merge**: Orchestrator for spawning and merging subplans (#184, In Review with PR #444).
-- **ACMS v1 full pipeline (M5 critical path)**: This is now the primary focus area. The specification mandates a 10-component Context Assembly Pipeline with Universal Knowledge Ontology (UKO), Context Request Protocol (CRP), pluggable context strategies (keyword, semantic, graph, temporal), strategy coordinator/fusion engine, scoped backend view filtering, skeleton compressor, and hot/warm/cold tiered storage with per-actor scoped views. 14 open issues in M5 (#188-#200, #258, #259) cover this work — all currently unassigned.
-- **Config service**: Multi-level configuration resolution with project-scoped overrides (#258, #259). Deferred from M2 to M5.
+- **Decision recording service**: Wire decision recording into the strategize/execute phases so decisions are automatically captured during plan execution (#172, In Progress, PR #433 pending merge).
+- **Plan explain CLI**: Plan tree and explain commands for decision tree visualization (#174, In Progress, PR #464 pending merge).
+- **ACMS v1 full pipeline (M5 — critical path)**: This is the primary focus area. The specification mandates a 10-component Context Assembly Pipeline with Universal Knowledge Ontology (UKO), Context Request Protocol (CRP), pluggable context strategies (keyword, semantic, graph, temporal), strategy coordinator/fusion engine, scoped backend view filtering, skeleton compressor, and hot/warm/cold tiered storage with per-actor scoped views. ~15 open feature issues in M5 (#188-#199, #259, #498, #499) cover this work. UKO (#189, PR #466) and ACMS pipeline (#188, PR #465) are In Review (Hamza). Config service (#258) merged. New: ACMS backend protocols (#498, Hamza) and context CLI wiring (#499, Jeff) created from spec gap analysis.
+- **Project-scoped config overrides**: Multi-level configuration with project-scoped overrides (#259). Config service base (#258) is done.
 - **Estimation actor logic**: The `estimation_actor` field is plumbed through Plan, Action, CLI, and service layers, but no actual estimator implementation exists to compute cost/risk estimates before execution (#209).
 - **Large-project context management**: Indexing 10,000+ file codebases with bounded memory context assembly, skeleton compression for parent-to-child context propagation, and performance validation at scale (#205, #208).
-- **Autonomy hardening (M6)**: Checkpointing and rollback integration (#206, In Review), semantic validation service (#207, In Review), autonomy guardrails and audit trail (#204, In Review), LSP server stub (#203), server client stubs (#201), async command execution (#312, #313), CLI polish (#210).
-- **Post-MVP deferred work (v3.6.0)**: Database resources (#342), cloud infrastructure resources (#343), safety profile enforcement (#345), permission system (#344, In Review), TUI/Web interface (#341), auth/team commands (#340), remote project support (#338), client stubs (#335-#337), virtual resource types (#329-#334).
-- **E2E smoke test suites**: M5 E2E suite (#406, In Review). M6 E2E suite (#457) now merged. Semantic validation test suites (#316) remain.
+- **Autonomy hardening (M6)**: Checkpointing and rollback integration (#206, In Review with PR #445), LSP server stub (#203), server client stubs (#201), async command execution (#312, #313), CLI polish (#210), LLM trace observability (#500, Jeff), ACP facade wiring (#501, Jeff). Autonomy guardrails (#204) and semantic validation (#207) already merged.
+- **Post-MVP deferred work (v3.6.0)**: Database resources (#342), cloud infrastructure resources (#343), safety profile enforcement (#345, PR #450 in review), TUI/Web interface (#341), auth/team commands (#340), remote project support (#338), client stubs (#335-#337), virtual resource types (#329-#334).
+- **E2E milestone validation suites**: M3 E2E (#494), M4 E2E (#495), M5 E2E (#496), M6 E2E (#497) validation issues remain open. Semantic validation test suites (#316) remain.
+- **Test infrastructure**: Feature file consolidation (#485) and ASV test suite runtime benchmarks (#486) still open under test perf Epic #478.
 
 The following areas are substantially implemented and are no longer blocking:
 
@@ -2063,56 +2071,66 @@ The following areas are substantially implemented and are no longer blocking:
 
 **Key remaining work**: None — milestone complete.
 
-#### Milestone 3: Decisions + Validations + Invariants (Target: Feb 26, ETA: ~Mar 2)
+#### Milestone 3: Decisions + Validations + Invariants (Target: Feb 26, ETA: ~Mar 3)
 
 **Goal**: Decisions are recorded during Strategize and Execute phases and persisted to the database. Users can view the decision tree (`plan tree`), inspect individual decisions (`plan explain`), manage invariants (`invariant add/list/remove`), and correct decisions (`plan correct --mode revert|append`) with selective subtree recomputation.
 
-**Current status**: **~87% complete** (2 open out of ~16 total M3 issues). Decision persistence merged (#171). Decision service wiring merged (#461). Validation pipeline and gating merged (#175, #176). DoD gating merged (#178). Diff review artifacts merged (#303). M3 E2E suites merged (#179, #180, #404). Invariant enforcement merged (#173).
+**Current status**: **~85% complete** (6 open / 39 total including PRs). Decision persistence merged (#171). Decision service wiring merged (#461). Validation pipeline and gating merged (#175, #176). DoD gating merged (#178). Diff review artifacts merged (#303). M3 E2E suites merged (#179, #180, #404). Invariant enforcement merged (#173). Test suite performance optimized 90%+ (#479-#483/PR #493 merged).
 
 **Key remaining work**:
 
-- Decision recording during strategize/execute phases (#172, Hamza — In Progress, PR #433)
-- Plan tree and explain CLI commands (#174, Hamza — In Progress, PR #464)
+- Decision recording during strategize/execute phases (#172, Hamza — PR #433 pending merge)
+- Plan tree and explain CLI commands (#174, Hamza — PR #464 pending merge)
+- M3 E2E milestone validation (#494, Brent)
+- Test consolidation (#485) and ASV test benchmarks (#486) under Epic #478
 
-#### Milestone 4: Corrections + Subplans + Checkpoints (Target: Mar 2, ETA: ~Mar 4)
+#### Milestone 4: Corrections + Subplans + Checkpoints (Target: Mar 2, ETA: ~Mar 3)
 
 **Goal**: Plans can spawn child plans (subplans) during execution. Subplans execute in parallel with configurable concurrency limits. Results are merged back using three-way merge strategies. Correction engine supports revert and append modes. Checkpointing enables rollback to previous plan states.
 
-**Current status**: **~95% complete** (1 open out of ~21 total M4 issues). DoD gating (#178), error recovery (#186), security hardening (#319, #320, #321), M4 E2E suites (#405, #187), sandbox checkpoint hooks (#462), invariant template hardening (#322) all merged and closed.
+**Current status**: **Feature-complete** (2 open / 44 total). Subplan execute+merge (#184) merged Mar 1. DoD gating (#178), error recovery (#186), security hardening (#319, #320, #321), M4 E2E suites (#405, #187), sandbox checkpoint hooks (#462), invariant template hardening (#322) all merged.
 
 **Key remaining work**:
 
-- Subplan execution and merge (#184, Luis — In Review, PR #444)
+- M4 E2E milestone validation (#495, Brent)
+- Security & Safety Hardening Epic (#362) closure verification
 
-#### Milestone 5: ACMS v1 + Context Scaling (Target: Mar 6, ETA: ~Mar 10)
+#### Milestone 5: ACMS v1 + Context Scaling (Target: Mar 6, ETA: ~Mar 11)
 
 **Goal**: The Advanced Context Management System v1 is operational. Projects with 10,000+ files can be indexed and queried. The context assembly pipeline produces scoped, budget-constrained context views for actors. Hot/warm/cold storage tiers manage context lifecycle.
 
-**Current status**: **~12% complete** (15 open out of ~17 total M5 issues). UKO/RDF groundwork started (Hamza, PRs #465/#466 in review). Context assembly pipeline in progress.
+**Current status**: **~18% complete** (~15 open feature issues out of ~18 total M5). Config service merged (#258). UKO/RDF groundwork started (Hamza, PRs #465/#466 in progress). Plan-subplan tool PR #463 in progress (Aditya). Coverage improvements (#475) merged.
 
 **Key remaining work**:
 
 - UKO ontology scaffolding (#189, Hamza — In Progress, PR #466)
 - ACMS v1 context pipeline (#188, Hamza — In Progress, PR #465)
-- CRP protocol for actor context requests (#199, Jeff)
-- Context strategies — keyword, semantic, graph, temporal (#208, #209, Jeff)
-- Plan-subplan tool and decision emission (#198, Aditya, PR #463)
-- M5 E2E ACMS integration suite (#406, Brent — In Review, PR #456)
+- CRP protocol models (#190), context strategy registry (#191), strategy coordinator (#192), scoped backend views (#193), skeleton compressor (#194) — all Hamza/Jeff
+- ACMS backend protocols (#498, Hamza), context CLI wiring (#499, Jeff)
+- Repo indexing service (#195), subplan service (#197), subplan tool (#198, Aditya PR #463), multi-project subplans (#199) — Jeff/Aditya
+- Project-scoped config overrides (#259, Jeff)
+- M5 E2E validation (#496, Brent)
 
-#### Milestone 6: Autonomy Hardening + Server Stubs (Target: Mar 10, ETA: ~Mar 12)
+#### Milestone 6: Autonomy Hardening + Server Stubs (Target: Mar 10, ETA: ~Mar 13)
 
 **Goal**: The system can autonomously execute a large-scale task (e.g., porting a substantial codebase) using hierarchical plan decomposition with 4+ levels of subplans, decision correction with selective subtree recomputation, parallel execution scaling to 10+ concurrent subplans, and validation-gated apply. Client-side server stubs are in place for future connectivity.
 
-**Current status**: **~32% complete** (13 open out of ~19 total M6 issues). M6 E2E suite merged (#457). Security enforcement (#436), async cleanup (#435) merged. Coverage improvements (#468) merged.
+**Current status**: **~52% complete** (13 open / 27 total M6 issues). Autonomy guardrails (#204), semantic validation (#207), permission system all merged. M6 E2E suite (#457) and M5 E2E suite (#469) merged. Security enforcement (#436), async cleanup (#435) merged.
 
 **Key remaining work**:
 
-- Hierarchical decomposition — recursive subplan planning (#335, #336, Jeff)
-- Autonomous estimation — cost/risk/time (#337, Jeff)
-- Autonomy guardrails and audit trail (#204, Luis — In Review, PR #443)
 - Checkpointing and rollback (#206, Luis — In Review, PR #445)
-- Semantic validation service (#207, Luis — In Review, PR #449)
-- M6 E2E autonomy acceptance suite (#211, Brent — In Review, PR #470)
+- Large-project decomposition (#205, Jeff)
+- Hot/warm/cold tiers and actor views (#208, Jeff)
+- Cost and risk estimation actor (#209, Jeff)
+- LSP server stub (#203, Jeff)
+- Server client stubs (#201, Jeff)
+- Async command execution (#312, #313, Jeff)
+- CLI polish (#210, Brent)
+- LLM trace observability (#500, Jeff)
+- ACP facade wiring (#501, Jeff)
+- Semantic validation test suites (#316, Brent)
+- M6 E2E validation (#497, Brent)
 
 ### Beyond Day 38: Extended Roadmap
 
@@ -2138,9 +2156,9 @@ Final refinements to achieve the complete specification:
 
 ### Schedule Risk Summary
 
-The project is currently running approximately **3-5 days behind** the original aggressive schedule, narrowed from 5-7 days at Day 18 and 7-9 days at Day 16. The primary causes of the original delay were: (1) the scope of v2-to-v3 architectural transition was larger than anticipated; (2) CI/CD pipeline stabilization consumed more effort than planned; and (3) the execute/apply pipeline was deferred in favor of breadth-first foundation work.
+The project is currently running approximately **3-4 days behind** the original aggressive schedule, narrowed from 3-5 days at Day 20 and 5-7 days at Day 18. The primary causes of the original delay were: (1) the scope of v2-to-v3 architectural transition was larger than anticipated; (2) CI/CD pipeline stabilization consumed more effort than planned; and (3) the execute/apply pipeline was deferred in favor of breadth-first foundation work.
 
-The gap has been **actively narrowing** since Day 16 and accelerated through Days 19-20: (a) M1 and M2 are now **fully complete** — all issues closed including MCP adapter, agent skills, skill CLI, MCP hooks, and FakeListLLM fix; (b) M3 is down to 2 issues (both Hamza's, both with PRs in review); (c) M4 has only 1 issue remaining (Luis's subplan execution, PR in review); (d) the workload redistribution to Jeff continues to pay dividends; (e) Rui returned from leave on Feb 27 and is available for testing work; (f) Luis has 6 PRs open across M4-M6+ representing substantial in-flight work.
+The gap has **continued narrowing** through Days 21-22: (a) M4 is now **feature-complete** — subplan execute+merge merged Mar 1; (b) M3 is down to 2 feature issues (both Hamza's, PRs pending merge); (c) test suite runtime reduced by 90%+ enabling faster iteration; (d) autonomy guardrails, semantic validation, and permission system all landed for M6; (e) config service merged, unblocking M5 config overrides; (f) Rui is available for M5+ testing. The critical path is now M5 (ACMS pipeline) with ~15 open issues and 4 days to target.
 
 !!! note "Server Mode"
 
@@ -2152,13 +2170,13 @@ The gap has been **actively narrowing** since Day 16 and accelerated through Day
 
 | Developer | Role | Primary Focus Areas | Notes |
 |-----------|------|---------------------|-------|
-| **Jeff** (freemo) | CTO/Lead Architect | M5-M6 feature work (ACMS, context strategies, autonomy, decomposition) | Fastest developer — 23 open issues, 199 story points remaining across M5-M6+ |
-| **Luis** (CoreRasurae) | Senior Python Architect | Subplan execution (#184), checkpointing (#206), semantic validation (#207), autonomy guardrails (#204) | 6 PRs open across M4-M6+; 8 open issues, 68 story points remaining |
-| **Aditya** (aditya) | Domain Expert (Agents/LLMs) | Plan-subplan tool (#198, PR #463) | M2 track complete; 1 open issue in M5 |
-| **Hamza** (hamza.khyari) | Python/RDF Expert | Decision recording (#172), plan explain (#174), ACMS pipeline (#188), UKO ontology (#189) | 4 PRs in progress/review; 11 open issues, M3 critical path |
-| **Rui** (rui.vieira) | Fast Developer | Testing (Behave/Robot), M5+ integration test suites | Returned from leave 2026-02-27; available for test assignments |
-| **Brent** (brent.edwards) | Quality Specialist | M5 E2E suite (#406), M6 E2E suite (#211, PR #470), coverage enforcement | 4 open issues; detail-oriented — owns all milestone verification testing |
-| **Mike** (mngrif) / **Brian** (brian) | Sysadmins | Deployment, infrastructure setup, CI/CD | Minimal coding tasks; ASV runner fix merged (#388) |
+| **Jeff** (freemo) | CTO/Lead Architect | M5 ACMS pipeline components, M6 autonomy hardening, architecture | Fastest developer — carries bulk of M5-M6 feature work; config service and test perf recently merged |
+| **Luis** (CoreRasurae) | Senior Python Architect | Checkpointing (#206, PR #445), server/LSP stubs (#201, #203), subplan service (#197) | Subplan execution merged Mar 1; autonomy guardrails and semantic validation merged; 3 PRs open |
+| **Aditya** (aditya) | Domain Expert (Agents/LLMs) | Plan-subplan tool (#198, PR #463) | M2 track complete; 1 active PR in M5 |
+| **Hamza** (hamza.khyari) | Python/RDF Expert | Decision recording (#172, PR #433), plan explain (#174, PR #464), ACMS pipeline (#188, PR #465), UKO (#189, PR #466) | 4 PRs active; M3 + M5 ACMS critical path owner; RDF/ontology expert |
+| **Rui** (rui.vieira) | Fast Developer | Testing (Behave/Robot), M5+ integration test suites | Returned from leave 2026-02-27; available for M5+ test assignments |
+| **Brent** (brent.edwards) | Quality Specialist | E2E milestone validation (#494-#497), test infrastructure (#485, #486), CLI polish (#210), semantic validation tests (#316) | Detail-oriented — owns all milestone verification testing and QA |
+| **Mike** (mngrif) / **Brian** (brian) | Sysadmins | Deployment, infrastructure setup, CI/CD | Minimal coding tasks |
 
 ## Weekly Development Schedules
 
@@ -2232,10 +2250,12 @@ The gap has been **actively narrowing** since Day 16 and accelerated through Day
 | Risk | Mitigation | Owner |
 |------|------------|-------|
 | ~~Apply pipeline completion (#155)~~ | ~~RESOLVED — merged Day 18~~ | ~~Luis~~ |
-| ~~MCP adapter + agent skills merge~~ | ~~RESOLVED — all merged Days 19-20 (#434, #453, #454, #455, #460)~~ | ~~Aditya~~ |
-| M3 decision recording + plan explain | Hamza has both PRs (#433, #464) in review; Jeff available to assist | Hamza + Jeff (reviewer) |
-| M5 ACMS pipeline critical mass | 15 open issues; Hamza has ACMS/UKO PRs in progress; Jeff carries 7 M5 items | Jeff + Hamza |
-| Luis PR throughput (6 open PRs) | Luis has substantial in-flight work across M4-M6+; prioritize M4 #184 first | Luis + Jeff (reviewer) |
+| ~~MCP adapter + agent skills merge~~ | ~~RESOLVED — all merged Days 19-20~~ | ~~Aditya~~ |
+| ~~M4 subplan execution (#184)~~ | ~~RESOLVED — merged Day 21 (PR #444)~~ | ~~Luis~~ |
+| ~~Autonomy guardrails + semantic validation~~ | ~~RESOLVED — #204 and #207 merged Days 20-21~~ | ~~Luis~~ |
+| M3 decision recording + plan explain | Hamza has both PRs (#433, #464) pending merge; Jeff prioritize reviews | Hamza + Jeff (reviewer) |
+| M5 ACMS pipeline critical path | ~15 open issues with 4 days to target; Hamza has UKO/ACMS PRs; Jeff carries architectural items | Jeff + Hamza |
+| Hamza bottleneck (M3 + M5) | Hamza owns M3 PRs AND M5 ACMS/UKO — must close M3 PRs before focusing on M5 | Hamza + Jeff (reviewer) |
 | Large codebase performance | Profile ACMS indexing + hot/warm/cold tiers; enforce bounded memory tests | Jeff + Hamza |
 | Rui ramp-up after return | Rui returned Feb 27; assign Behave/Robot test suites for M5+; pair with Brent | Rui + Brent |
 | Server connectivity stubs stability | Keep client-only stubs isolated; gate with feature flags and contract tests | Jeff |
@@ -3160,3 +3180,210 @@ Note: Each cell is **completed/total story points** for that milestone/owner per
 | M6 | 13/92 | - | 0/39 | - | 25/30 | - | - | 38/161 |
 | M6+ | 0/64 | - | 0/24 | 0/29 | 0/5 | - | 8/8 | 8/130 |
 | **Total** | **487/686** | **214/222** | **95/163** | **69/145** | **160/176** | **0/0** | **108/108** | **1133/1500** |
+
+### 2026-03-02 (Day 22 since kickoff on 2026-02-09)
+
+**Summary**
+
+- Timeline reference: Day 7/M1 = 2026-02-15, Day 14/M2 = 2026-02-22, Day 18/M3 = 2026-02-26, Day 22/M4 = 2026-03-02, Day 26/M5 = 2026-03-06, Day 30/M6 = 2026-03-10
+- Status: Behind ~3-4d
+- Deadline risk: MEDIUM (narrowing from HIGH)
+- Overall completion: ~88% (~360/410 milestone issues closed, excluding Epics/Legendaries)
+
+**Notes**
+
+- **M4 feature-complete**: Subplan execute+merge (#184/PR #444) merged Mar 1 — M4 now has 42 closed, 2 open (Epic #362 + E2E #495)
+- **Config service merged**: Multi-level resolution (#258/PR #474) merged Mar 1 — unblocks M5 project-scoped overrides (#259)
+- **Test suite 90%+ faster**: BDD 26min→2min, coverage 75min→5min (#479-#483/PR #493 merged Mar 2). Coverage improved to 98%.
+- **M6 progress**: Autonomy guardrails (#204), semantic validation (#207), permission system all merged Days 20-21. Checkpoint/rollback (#206, PR #445) In Review.
+- **Hamza bottleneck**: Has 4 active PRs spanning M3 (#433, #464) and M5 (#465, #466). M3 PRs must close before M5 ACMS work can accelerate.
+- **Luis freed up**: Subplan execution merged; autonomy guardrails and semantic validation merged. Now available for M6 items.
+- **Rui available**: Returned Feb 27, available for Behave/Robot test suites for M5+.
+- **M5 is the critical path**: ~15 open feature issues with only 4 days to Mar 6 target. ACMS pipeline requires UKO, CRP, strategies, coordinator, backend views, and compressor.
+
+#### Milestone forecast 
+
+| Milestone | Target -> ETA | Delta | Risk |
+|-----------|---------------|-------|------|
+| M1 (v3.0.0) | (2026-02-15) -> Done | +13d actual | COMPLETE |
+| M2 (v3.1.0) | (2026-02-22) -> Done | +6d actual | COMPLETE |
+| M3 (v3.2.0) | (2026-02-26) -> ETA 2026-03-03 | +5d | LOW-MED — 2 feature PRs pending merge (Hamza) + E2E validation |
+| M4 (v3.3.0) | (2026-03-02) -> ETA 2026-03-03 | +1d | LOW — feature-complete; only E2E validation + Epic closure remain |
+| M5 (v3.4.0) | (2026-03-06) -> ETA 2026-03-11 | +5d | HIGH — ~15 open issues; ACMS pipeline is critical path; 4 days to target |
+| M6 (v3.5.0) | (2026-03-10) -> ETA 2026-03-13 | +3d | MEDIUM — 11 open feature issues; autonomy/validation already landed; Luis freed up |
+
+#### Track forecast 
+
+| Track | Status | ETA | Risk | Blocking |
+|-------|--------|-----|------|----------|
+| Track A (Plan lifecycle) | **complete** | Done | LOW | none |
+| Track B (Resources + sandbox) | **complete** | Done | LOW | none |
+| Track C (Actors/tools/skills/MCP) | **complete** | Done | LOW | none |
+| Track D (Decisions/validations) | behind ~5d | ETA 2026-03-03 | LOW-MED | decision recording (#172, PR #433) + plan explain (#174, PR #464) — both Hamza, PRs pending merge |
+| Track E (Corrections/subplans) | **complete** | Done | LOW | subplan execute+merge merged Mar 1 |
+| Track F (ACMS/context) | in progress | ETA 2026-03-11 | HIGH | ACMS pipeline (#188) + UKO (#189) + CRP (#190) + strategies (#191, #192) — Hamza blocked on M3 PRs first |
+| Track Q (Quality automation) | **complete** | Done | LOW | test suite 90%+ faster; maintenance only |
+| Track T (Testing) | strong progress | ETA ongoing | LOW-MED | M3/M4/M5/M6 E2E validation issues (#494-#497) remain; Rui available |
+
+#### Developer forecast 
+
+| Name | Days Ahead/Behind | Availability | Risk | Focus |
+|------|-------------------|--------------|------|-------|
+| Jeff | +3d ahead (throughput remains exceptional; config service + test perf merged Days 21-22) | available | MEDIUM | M5 ACMS architectural items (#192, #195, #259), M6 decomposition/estimation (#205, #208, #209), M6 stubs (#201, #203) |
+| Luis | on track (subplan merged, autonomy+validation merged; freed from M4 blockers) | available | LOW-MED | M6 checkpoint (#206, PR #445 in review), subplan service (#197), server/LSP stubs (#201, #203) |
+| Hamza | -2d behind (4 active PRs; M3 PRs must merge before M5 focus) | available | MEDIUM-HIGH | M3 decision recording (#172, PR #433), plan explain (#174, PR #464), then M5 UKO (#189), ACMS pipeline (#188), CRP (#190) |
+| Aditya | on track (25/26 closed = 96%; 1 active PR) | available | LOW | M5 plan-subplan tool (#198, PR #463) |
+| Brent | +1d ahead (E2E suites merged, test infra strong) | available | LOW | E2E milestone validation (#494-#497), test consolidation (#485, #486), CLI polish (#210), semantic validation tests (#316) |
+| Rui | N/A (returned Feb 27; ramping up) | available | LOW-MED | Behave/Robot test suites for M5+ features |
+| Mike/Brian | N/A | standby | LOW | none |
+
+#### Task inventory 
+
+Milestone per developer as of the current date.
+Note: Each cell is **completed/total issues** for that milestone/owner per Forgejo tracker. Epics and Legendaries excluded. PRs excluded.
+
+| Milestone | Jeff | Aditya | Luis | Hamza | Brent | Rui | Unassigned | Total |
+|-----------|------|--------|------|-------|-------|-----|------------|-------|
+| M1 | 27/27 | 12/12 | 2/2 | 4/4 | 10/10 | 0/0 | 97/97 | 152/152 |
+| M2 | 24/24 | 13/13 | 4/4 | 1/1 | 5/5 | 0/0 | 52/52 | 99/99 |
+| M3 | 7/7 | 0/0 | 2/2 | 2/4 | 3/3 | 0/0 | 5/5 | 19/21 |
+| M4 | 8/8 | 0/0 | 4/4 | 4/4 | 5/5 | 0/0 | 1/1 | 22/22 |
+| M5 | 2/8 | 0/1 | 0/0 | 0/5 | 1/3 | 0/0 | 1/1 | 4/18 |
+| M6 | 2/10 | 0/0 | 2/4 | 0/0 | 4/5 | 0/0 | 0/0 | 8/19 |
+| M6+ | 0/8 | 0/0 | 0/3 | 0/4 | 0/1 | 0/0 | 1/1 | 1/17 |
+| **Total** | **70/92** | **25/26** | **14/19** | **11/22** | **28/32** | **0/0** | **157/157** | **305/348** |
+
+#### Story point allocation 
+
+Story points per developer per milestone.
+Note: Each cell is **completed/total story points** for that milestone/owner per Forgejo tracker. Issues without a `Points/X` label or milestone are excluded. Epics and Legendaries (organizational items) are excluded.
+
+| Milestone | Jeff | Aditya | Luis | Hamza | Brent | Rui | Unassigned | Total |
+|-----------|------|--------|------|-------|-------|-----|------------|-------|
+| M1 | 188/188 | 128/128 | 16/16 | 19/19 | 71/71 | - | 95/95 | 517/517 |
+| M2 | 176/176 | 86/86 | 29/29 | 5/5 | 21/21 | - | - | 317/317 |
+| M3 | 58/58 | - | 21/21 | 13/23 | 11/11 | - | 47/47 | 150/160 |
+| M4 | 47/47 | - | 34/34 | 32/32 | 24/24 | - | 1/1 | 138/138 |
+| M5 | 13/61 | 0/8 | - | 0/37 | 8/14 | - | 4/4 | 25/124 |
+| M6 | 13/92 | - | 18/39 | - | 25/30 | - | - | 56/161 |
+| M6+ | 0/64 | - | 0/24 | 0/29 | 0/5 | - | 8/8 | 8/130 |
+| **Total** | **495/686** | **214/222** | **118/163** | **69/145** | **160/176** | **0/0** | **155/155** | **1211/1547** |
+
+---
+
+## Tracker Maintenance Log
+
+### 2026-03-02 (Day 22) — Full Tracker Synchronization
+
+Performed a comprehensive Forgejo tracker audit and synchronization against `docs/specification.md`. All changes below were made via the Forgejo API (MCP tools and direct REST calls).
+
+#### 1. Organizational Issue Assignments
+
+All 8 Legendaries and 15 open Epics assigned to `freemo` (Jeff) for accountability:
+
+- **Legendaries**: #370, #372, #374, #375, #376, #378, #389, #390
+- **Epics**: #352, #362, #367, #368, #369, #392, #394, #395, #396, #397, #398, #399, #400, #401, #478
+
+#### 2. Feature/Test Issue Assignments (M3-M6)
+
+25 high-priority feature and testing issues assigned to their respective developers:
+
+- **freemo** (Jeff): #190, #192, #194, #197, #199, #201, #203, #205, #208, #209, #259, #312, #313, #499, #500, #501
+- **hamza.khyari** (Hamza): #188, #189, #191, #193, #195, #498
+- **aditya** (Aditya): #198
+- **brent.edwards** (Brent): #210, #316, #494, #495, #496, #497
+- **CoreRasurae** (Luis): #206
+
+#### 3. ACMS Pipeline Priority Promotion
+
+Issues #188-#192 promoted from `MoSCoW/Should have` + `Priority/Medium` to `MoSCoW/Must have` + `Priority/High` to reflect their critical-path status for M5:
+
+| Issue | Title |
+|-------|-------|
+| #188 | feat(acms): add ACMS v1 context pipeline |
+| #189 | feat(uko): add UKO ontology scaffolding |
+| #190 | feat(acms): add context request protocol models |
+| #191 | feat(acms): add context strategy registry |
+| #192 | feat(acms): add strategy coordinator and fusion engine |
+
+#### 4. State Label Corrections
+
+Issues with open PRs corrected from `State/In Progress` to `State/In Review`:
+
+| Issue | PR | Title |
+|-------|----|-------|
+| #188 | #465 | ACMS v1 context pipeline |
+| #189 | #466 | UKO ontology scaffolding |
+| #174 | #464 | Plan explain and decision tree outputs |
+| #172 | #433 | Decision recording and snapshot store |
+
+#### 5. New Issues from Spec Gap Analysis
+
+4 new issues created from specification-vs-codebase gap analysis. All labeled `State/Verified`, `Type/Feature`, `Priority/Medium`, `MoSCoW/Should have`, `Points/8`:
+
+| Issue | Milestone | Assignee | Title |
+|-------|-----------|----------|-------|
+| #498 | M5 (v3.4.0) | hamza.khyari | feat(acms): add text, vector, and graph backend protocol implementations |
+| #499 | M5 (v3.4.0) | freemo | feat(cli): wire project context CLI stubs to ACMS pipeline |
+| #500 | M6 (v3.5.0) | freemo | feat(observability): add LLMTrace model and operational metrics |
+| #501 | M6 (v3.5.0) | freemo | feat(acp): wire ACP local facade handlers to live services |
+
+#### 6. MoSCoW Label Additions
+
+E2E validation issues #494-#497 were missing `MoSCoW/Should have` — added.
+
+#### 7. Dependency Graph (26 blocking links)
+
+Created via direct REST API calls to `POST /api/v1/repos/{owner}/{repo}/issues/{blocker}/blocks` with `IssueMeta` body format (`{"owner","repo","index"}`). The dependency graph encodes the specification's layered architecture.
+
+**M3 Chain** (decision recording -> plan explain -> E2E):
+
+```
+#172 (decision recording) --blocks--> #174 (plan explain)
+#172 --blocks--> #494 (M3 E2E)
+#174 --blocks--> #494
+```
+
+**M5 ACMS Critical Chain** (specification Section 14 layered pipeline):
+
+```
+#189 (UKO) --> #190 (CRP models) --> #191 (strategy registry) --> #192 (coordinator+fusion) --> #188 (full pipeline)
+#189 --> #498 (backend protocols) --> #191
+#498 --> #193 (scoped views) --> #188
+#190 --> #194 (skeleton compressor) --> #188
+#189 --> #195 (repo indexing)
+#188 --> #499 (context CLI wiring)
+#188 --> #496 (M5 E2E)
+```
+
+**M5 Subplan Chain**: `#197 (subplan service) --> #199 (multi-project subplans)`
+
+**M6 Dependencies on M5**:
+
+```
+#188 (ACMS pipeline) --> #205 (large-project decomposition) --> #497 (M6 E2E)
+#188 --> #208 (hot/warm/cold tiers) --> #497
+#188 --> #501 (ACP facade wiring) --> #201 (server client stubs)
+#500 (LLM trace) --> #209 (estimation actor) --> #497
+```
+
+#### 8. Verification Pass Results
+
+After all changes, every open issue (73 total) was audited:
+
+- **All open issues have**: a State label, a milestone (except Epics/Legendaries which correctly have none), an assignee, a MoSCoW label, a Priority label, and a Type label.
+- **State labels are correct**: PR-linked issues have `State/In Review`; actively worked issues have `State/In Progress`; all others have `State/Verified`.
+- **No orphaned issues**: All feature issues map to a parent Epic.
+- **Dependency graph complete**: 26 blocking links created covering the M3 decision chain, M5 ACMS layered pipeline, M5 subplan chain, M6 cross-milestone dependencies, and E2E validation gates.
+
+#### Summary of Open Issue Counts Post-Cleanup
+
+| Milestone | Open Feature | Open Testing | Open Epic/Legendary | Total Open |
+|-----------|-------------|-------------|---------------------|------------|
+| M3 (v3.2.0) | 2 | 1 | 1 | 4 |
+| M4 (v3.3.0) | 0 | 1 | 1 | 2 |
+| M5 (v3.4.0) | 16 | 1 | 2 | 19 |
+| M6 (v3.5.0) | 12 | 2 | 1 | 15 |
+| M6+ (v3.6.0) | 16 | 1 | 0 | 17 |
+| No Milestone | 0 | 0 | 16 | 16 |
+| **Total** | **46** | **6** | **21** | **73** |

mkdocs.yml

@@ -62,6 +62,8 @@ nav:
     - ADR-039 Container Resource Types: adr/ADR-039-container-resource-types.md
     - ADR-040 LSP Resource Types: adr/ADR-040-lsp-resource-types.md
     - ADR-041 Safety Profile Extraction: adr/ADR-041-safety-profile-extraction.md
+    - ADR-042 Resource Type Inheritance: adr/ADR-042-resource-type-inheritance.md
+    - ADR-043 Devcontainer Integration: adr/ADR-043-devcontainer-integration.md
 
 theme:
   name: material