bmad-module-skill-forge 0.10.0 → 0.10.1-alpha.0

package/src/skf-update-skill/steps-c/step-03-re-extract.md

@@ -0,0 +1,336 @@
+---
+nextStepFile: './step-04-merge.md'
+extractionPatternsData: 'skf-create-skill/references/extraction-patterns.md'
+extractionPatternsTracingData: 'skf-create-skill/references/extraction-patterns-tracing.md'
+remoteSourceResolutionData: 'references/remote-source-resolution.md'
+tierDegradationRulesData: 'skf-create-skill/references/tier-degradation-rules.md'
+---
+
+# Step 3: Re-Extract Changed Exports
+
+## STEP GOAL:
+
+Perform tier-aware extraction on only the changed files identified in step 02, producing fresh export data with confidence tier labels (T1/T1-low/T2) that will be merged into the existing skill in step 04.
+
+## Rules
+
+- Focus only on extracting changed exports — do not merge or modify existing skill
+- Only extract files in the change manifest — do not touch unchanged files. **Exception (gap-driven mode):** §0a's Targeted Re-Extraction Branch also scans files listed in each manifest entry's `remediation_paths[]` to resolve citation-less Critical/High gaps.
+- For each changed file, launch a subprocess for deep AST analysis (Pattern 2); if unavailable, extract sequentially
+
+## MANDATORY SEQUENCE
+
+**CRITICAL:** Follow this sequence exactly. Do not skip, reorder, or improvise unless user explicitly requests a change.
+
+### 0. Check for Gap-Driven Mode
+
+**If `update_mode == "gap-driven"` (set in step-01 via `--from-test-report`, confirmed in step-02 section 0):**
+
+Source code has not drifted — the gap-derived manifest from step-02 contains export-level findings translated from the test report, not file-level changes. Perform citation spot-checks instead of full re-extraction to verify each gap-affected export is still at its recorded location.
+
+**0.a Pre-flight: verify workspace HEAD matches pinned commit.** Gap-driven spot-checks read source at recorded `source_line` positions and must see the exact bytes the skill was pinned against. A drifted workspace silently verifies against the wrong tree — moved/renamed symbols appear "verified" because the recorded line now points at different code. Before reading any source, run this guard:
+
+- Resolve `pinned_commit` from `metadata.source_commit` (loaded in step-01).
+- **If `pinned_commit` is null, empty, `"local"`, or a per-repo map (stack skills) with no single commit:** skip the guard and log `workspace_drift_check: skipped (no pinned commit)`. Continue to bullet 1.
+- **If `source_root` is not a git working tree** (e.g., bare checkout, tarball extract) — detect by running `git -C "{source_root}" rev-parse --is-inside-work-tree`; non-zero exit means skip: log `workspace_drift_check: skipped (not a git working tree)`. Continue to bullet 1.
+- **Otherwise** run `git -C "{source_root}" rev-parse HEAD` and compare to `pinned_commit`. Accept either a full SHA match or a short-SHA prefix match (the pinned commit is often stored as an 8-char short hash — see `src/knowledge/provenance-tracking.md`).
+  - **On match:** log `workspace_drift_check: ok ({short_sha})` and continue.
+  - **On mismatch, AND the user did not pass `--allow-workspace-drift`:** HALT immediately with exit status `halted-for-workspace-drift`. Display:
+
+    ```
+    Workspace HEAD does not match the commit this skill was pinned against.
+
+      pinned (metadata.source_commit): {pinned_commit}
+      pinned ref (metadata.source_ref): {source_ref or "unset"}
+      workspace HEAD ({source_root}):  {head_sha}
+
+    Gap-driven spot-checks read source at pinned line numbers — verifying
+    against a drifted tree silently produces wrong results (symbols appear at
+    unintended locations). Re-sync the workspace before re-running:
+
+      git -C "{source_root}" checkout {source_ref or pinned_commit}
+
+    Or, to intentionally proceed against the current workspace HEAD (accepting
+    that spot-checks will read bytes that differ from the pinned commit),
+    re-run update-skill with `--allow-workspace-drift`.
+    ```
+
+    Do not proceed to bullet 1. Step-04 merge has not run; no partial writes.
+  - **On mismatch WITH `--allow-workspace-drift`:** log `workspace_drift_check: overridden (pinned={pinned_commit}, head={head_sha})` and surface a visible warning in the final report ("**Workspace drift accepted via --allow-workspace-drift** — spot-checks read HEAD {head_sha}, not pinned {pinned_commit}"). Continue to bullet 1. The override does not automatically re-pin `metadata.source_commit`; re-pinning is explicit user work (run the normal-mode update-skill flow against the same HEAD, or re-create the skill).
+
+1. Use the provenance map already loaded in step-01 (at `{forge_version}/provenance-map.json`) — do not re-read
+2. For each entry in the gap-derived change manifest from step-02:
+   - Look up the export by `name` in `provenance_map.exports` — read `source_file` and `source_line`
+   - **If export not found in provenance map:**
+     - **If the manifest entry has a `source_citation` (propagated from the test report by step-02 §0 bullet 4):** read the file at that citation's `file:line ± 5` lines and verify the symbol name still appears within that window. Record a full `verified` / `moved` / `missing` entry using the citation as the starting location — same spot-check logic as the "export found" branch below, keyed on the manifest-supplied citation instead of the provenance map. The export is still flagged `NEW_EXPORT` for the merge step; this branch only upgrades the provenance entry from `unknown` to a live spot-check result so step-06 writes `source_file` / `source_line` instead of `null`.
+     - **If the manifest entry has no `source_citation` but has a non-empty `remediation_paths[]` AND `severity` is `Critical` or `High`:** route this entry to §0a (Targeted Re-Extraction Branch). §0a scans the remediation paths with the tier-appropriate extractor and, on success, records a full verification record with `verification: re-extracted`, a live `provenance_citation`, and full signature/params/return-type fields for the merge step to consume as a NEW_EXPORT. On failure, §0a halts the workflow — Critical/High gaps are not allowed to degrade to `unknown`. See §0a for the procedure, the consolidated halt protocol, and the output record shape.
+     - **If the manifest entry has no `source_citation` AND (`remediation_paths[]` is empty OR `severity` is `Medium`, `Low`, or `Info`):** record as new (`provenance_citation: unknown`) — no spot-check possible; flag for merge step to handle as `NEW_EXPORT`. Step-06 §3 only accepts null `source_file` / `source_line` for these lower-severity unknowns; a Critical/High unknown reaching step-06 indicates §0a was skipped or bypassed and is a workflow bug.
+   - **If export found:** read the source file at `source_line ± 5` lines and verify the symbol name still appears within that window
+   - Record verification outcome: `verified` (symbol at recorded line), `moved` (symbol found elsewhere in same file — record new line), `missing` (symbol not found in file), `re-extracted` (resolved via §0a from `remediation_paths[]`), or `unknown` (no usable provenance data)
+3. Build a minimal extraction results block matching section 4's shape, with `mode: gap-driven` and per-export verification records:
+
+   ```
+   Extraction Results:
+     mode: gap-driven
+     files_extracted: {count}  # non-zero only when §0a scanned remediation_paths[]
+     exports_extracted: {gap_count}
+     confidence_breakdown:
+       T1: {verified_count + moved_count + re_extracted_t1_count}
+       T1-low: {re_extracted_t1_low_count}
+       T2: 0
+
+     Per-export verification:
+       {export_name}:
+         provenance_citation: {source_file}:{source_line}
+         verification: verified|moved|missing|unknown|re-extracted
+         new_location: {source_file}:{new_line}  # set when moved OR re-extracted
+         resolution_source: remediation-paths    # set only when verification == re-extracted
+         gap_category: NEW_EXPORT|MODIFIED_EXPORT|metadata_update
+
+     Per-file extractions:   # populated only when §0a produced re-extracted records
+       {file_path}:
+         exports:
+           - name: {export_name}
+             type: function|class|type|constant
+             signature: {full signature}
+             location: {file}:{start_line}-{end_line}
+             confidence: T1|T1-low
+             params: [{name, type}]
+             return_type: {type}
+             docstring: {summary}
+   ```
+
+4. Set `no_reextraction: true` in workflow context — step-06 will use this flag to skip stale `source_file`/`source_line`/`confidence` field updates for `verified` exports. `moved` exports get updated citations; `re-extracted` exports get full fresh provenance from §0a's extraction records (see step-06 §3). The flag is a global gap-driven marker, not a per-entry one — step-06 dispatches on each verification outcome independently.
+5. **Skip all remaining sections of step-03** — sections 1–5 are source-drift extraction paths that do not apply. Display the summary below and load `{nextStepFile}` to proceed directly to the merge step.
+
+"**Gap-driven re-extraction.** Verified {verified_count}/{gap_count} citations against live source. Moved: {moved_count}. Missing: {missing_count}. Re-extracted (via remediation paths, §0a): {re_extracted_count}. Unknown (not in provenance map): {unknown_count}. Proceeding to merge."
+
+**If normal mode (`update_mode` unset or not `gap-driven`):** Continue with docs-only check and source extraction below.
+
+### 0a. Targeted Re-Extraction Branch (Helper — Called from §0 bullet 2)
+
+**Do not execute this section sequentially.** It is a helper procedure invoked by §0 bullet 2 when specific conditions are met (see below). Normal-mode runs, and gap-driven runs where every entry has a `source_citation` or qualifies as `Medium`/`Low`/`Info` unknown, skip this section entirely. §0's "skip sections 1–5" instruction does not apply here — §0a is addressed by name from §0, not by sequential fall-through.
+
+**Used by:** §0 bullet 2, when a manifest entry has no `source_citation`, has non-empty `remediation_paths[]`, and `severity` is `Critical` or `High`.
+
+**Purpose:** produce AST-backed provenance for citation-less Critical/High gaps so step-06 §3 never writes `source_file: null` for blocking findings. Honors the workflow-level rule **Never hallucinate — every statement must have AST provenance** against the most common gap-driven trigger — a failing test report whose Gap Report `Source:` field is a region reference (e.g., `@storybook/addon-docs control primitives`) rather than a `file:line` pair. Gap-driven mode skips §1 through §5, so §0a is also the only place §1b's source-access and extraction machinery is invoked during gap-driven runs.
+
+**Procedure:**
+
+1. **Resolve source access** — invoke §1b's MCP-fallback chain (gh API → zread → deepwiki → workspace / ephemeral clone) once per workflow run to ensure files under `{source_root}` are readable. Cache the chosen access path; do not re-resolve per entry.
+2. **Expand `remediation_paths[]`** — for each path across all qualifying entries:
+   - Literal source file (ends in a recognized source extension): use as-is.
+   - Directory or glob: expand under `{source_root}` using the provenance map's file patterns.
+   - **Security boundary:** reject and skip any path that resolves outside `{source_root}`. Remediation text is user-editable and must never be allowed to escape the source tree.
+   - Deduplicate the resolved file set across all entries routed to §0a — each physical file is scanned at most once.
+3. **Extract** — run the tier-appropriate extractor from §1b (Quick pattern-match → T1-low; Forge/Forge+/Deep AST via ast-grep → T1) over the resolved file set. Launch subprocesses in parallel (Pattern 4) when available; sequential fallback otherwise. Follow the AST Extraction Protocol in `{extractionPatternsData}` for Forge/Deep tiers, and the tier-degradation rules in `{tierDegradationRulesData}` when AST tools fail on individual files.
+4. **Match by name** — for each manifest entry routed here, search the aggregated extraction results for an export whose `name` matches the manifest entry's `name`. Record the first hit as:
+   - `verification: re-extracted`
+   - `provenance_citation: {file}:{start_line}` from the AST result
+   - `new_location: {file}:{start_line}` (same value — satisfies the existing consumer contract)
+   - `resolution_source: remediation-paths`
+   - `confidence: T1` (AST-extracted) or `T1-low` (pattern-matched fallback)
+   - the full extraction signature (type, params, return_type, docstring) — mirror the shape of §4's per-file extraction record so step-04 Priority 5 can merge it with the same code path used in normal mode.
+5. **Track failures across all qualifying entries.** Collect every entry whose symbol was not found in any scanned remediation path into an `unresolved[]` list. After processing every qualifying entry, if `unresolved[]` is non-empty: HALT with a consolidated report listing every unresolved entry (`name`, `severity`, `remediation_paths`, `files_scanned`, `exports_found_in_scan`). Template:
+
+   ```
+   Targeted re-extraction failed for {N} Critical/High gap(s).
+
+   Critical and High gaps must resolve to AST provenance. The Remediation text for
+   the entries below does not name a file that contains the expected export, so the
+   workflow cannot produce a non-null `source_file` / `source_line` without
+   hallucinating.
+
+   Unresolved entries:
+     {for each entry in unresolved[]:}
+       - {name} ({severity})
+         remediation_paths: {paths}
+         files_scanned:     {count}
+         exports_matched:   0
+
+   Fix one of the following, then re-run update-skill:
+     a) Add a `file:line` citation to the Gap Report `Source:` field.
+     b) Edit the Remediation text to name the file(s) that actually contain the export(s).
+     c) Downgrade the gap(s) to Medium/Low/Info (accepts the degraded documentation outcome).
+   ```
+
+   Exit with status `halted-for-remediation-path`. Step-04 merge has not run; no partial writes.
+
+6. **Success summary** — record `targeted_reextraction: {resolved_count, files_scanned, exports_matched, tier}` in workflow context. The evidence report (step-06 §4) surfaces this alongside the verified / moved / missing tally.
+
+**Why halt instead of degrading to `unknown`:** a Critical or High gap by definition blocks skill usefulness — it is either missing documentation for a public API or a wrong signature. Silently writing `source_file: null` for a blocking gap produces a skill that passes re-test but still hides the broken behavior behind a placeholder. The halt forces the test report to carry usable remediation information — a one-time fix-up that is far cheaper than a downstream audit trying to track why the "repaired" skill still fails.
+
+### 1. Check for Docs-Only Mode
+
+**If `source_type: "docs-only"` in the original brief or metadata:**
+
+"**Docs-only skill detected.** This skill was generated from external documentation, not source code. Re-extraction will re-fetch the original `doc_urls` to check for updated content."
+
+- Re-fetch each URL from `doc_urls` (from the brief or metadata) using whatever web fetching capability is available
+- Extract updated API information with T3 `[EXT:{url}]` citations
+- Build the updated extraction inventory from fetched content
+- Skip all source code extraction below — proceed directly to the merge step (section 5 or equivalent)
+
+**If `source_type: "source"` (default):** Continue with source extraction below.
+
+### 1b. Determine Extraction Strategy by Tier
+
+**Remote Source Resolution (Forge/Deep only):**
+
+**MCP source access (ordered fallback):** When `source_repo` is set in metadata.json, try each MCP tool in order to fetch only the changed files from the change manifest. This avoids clone overhead entirely. Tools are ordered by data freshness — gh API returns live GitHub content and is preferred for update-skill where current file versions are required. zread and deepwiki depend on manual indexing and may return stale data if indexes haven't been refreshed since the changes being extracted.
+
+1. **gh API** — `gh api repos/{owner}/{repo}/contents/{path}` for raw file content
+   - If accessible: fetch file content (base64-decoded), always current
+   - If rate-limited, 404, or inaccessible: log tool and reason, continue to next tool
+2. **zread** — `get_repo_structure` + `read_file` for targeted file access
+   - If repo found: fetch changed files, proceed with extraction
+   - If "repo not found" or error: log tool and reason, continue to next tool
+   - Caveat: indexed data — may be stale if index wasn't refreshed after the target changes
+3. **deepwiki** — `ask_question` for targeted export/signature queries
+   - If repo indexed and returns usable source data: extract from response
+   - If no results or repo not indexed: log tool and reason, continue to next tool
+   - Caveat: returns synthesized content, not raw source — extraction quality varies; index may be stale
+
+**Confidence labeling:** MCP-fetched content written to a temp file and analyzed with ast-grep → T1. MCP-fetched content analyzed with pattern matching (AST unavailable) → T1-low.
+
+**If all MCP tools fail for this repo:** Fall back to workspace or ephemeral clone — load and follow `{remoteSourceResolutionData}` for clone setup, version reconciliation, and AST tool unavailability handling.
+
+**If all approaches fail (MCP + workspace/ephemeral clone):** Degrade to provenance-map-only analysis (State 2, T1 confidence from compilation-time data). Warn user: "Source access failed for {source_repo}. Analysis limited to provenance-map baseline."
+
+**Quick tier (text pattern matching):**
+- Extract function/class/type names via regex patterns
+- Extract export statements via text matching
+- Confidence: T1-low (pattern-matched, not AST-verified)
+
+**Forge tier (AST structural extraction):**
+
+⚠️ **CRITICAL:** Load and follow the **AST Extraction Protocol** from `{extractionPatternsData}`. Use the decision tree based on the number of changed files: prefer MCP `find_code()` for small sets, `find_code_by_rule()` with scoped YAML rules for medium sets, and CLI `--json=stream` with line-by-line streaming for large sets. Never use `ast-grep --json` (without `=stream`) — it loads the entire result set into memory and will fail on large codebases.
+
+- Extract: function signatures, type definitions, class members, exported constants
+- Extract: parameter types, return types, JSDoc/docstring comments
+- Confidence: T1 (AST-verified structural truth)
+
+**Tier degradation handling (Forge/Forge+/Deep):** If ast-grep is unavailable or fails on individual files, follow `{tierDegradationRulesData}` for fallback strategy and user notification requirements. Silent degradation is forbidden — the user must always know when AST extraction was skipped.
+
+**Deep tier (AST + QMD semantic enrichment):**
+- Perform all Forge tier extractions (T1)
+- Additionally: launch a subprocess that queries qmd_bridge for temporal context on changed exports, returning T2 evidence per export
+- QMD provides: usage patterns, historical context, related documentation
+- Confidence: T1 for structural, T2 for semantic enrichment
+
+**Tool resolution:** `ast_bridge` → ast-grep MCP tools (`find_code`, `find_code_by_rule`) or `ast-grep` CLI. `qmd_bridge` → QMD MCP tools (`mcp__plugin_qmd-plugin_qmd__search`, `vector_search`) or `qmd` CLI. See `knowledge/tool-resolution.md`.
+
+### 2. Extract Changed Files
+
+**Skip authoritative doc paths.** Before iterating the change manifest, build a skip set from `promoted_docs_new[]` (populated by step-02 §1b) and any existing `file_entries[]` entries with `file_type: "doc"` from the provenance map. These are documentation files tracked for drift detection only — they must not reach AST extraction, which would produce ghost entries on non-code content. If a change manifest entry matches the skip set, skip it silently and continue; doc-type drift is handled by step-02 Category D and step-04 Priority 6/7.
+
+DO NOT BE LAZY — For EACH remaining file in the change manifest with status MODIFIED, ADDED, or RENAMED, launch a subprocess that:
+
+1. Loads the source file
+2. Performs tier-appropriate extraction (Quick/Forge/Forge+/Deep)
+3. For each export found:
+   - Record: export name, type (function/class/type/constant), signature
+   - Record: file path, start line, end line
+   - Record: parameters with types (if function/method)
+   - Record: return type (if function/method)
+   - Record: JSDoc/docstring summary (if present)
+   - Label: confidence tier (T1/T1-low/T2)
+4. Returns structured extraction findings to parent
+
+**For DELETED files:** No extraction needed — deletions handled in merge step.
+
+**For MOVED files:** Re-extract at new location to update file:line references.
+
+**Re-export tracing (Forge/Deep only):** After extracting changed files, check if any public exports from the package entry point (`__init__.py`, `index.ts`, `lib.rs`) are unresolved — particularly when a changed file is part of a module re-export chain. Follow the **Re-Export Tracing** protocol in `{extractionPatternsTracingData}` to trace unresolved symbols to their actual definition files.
+
+### 2b. CCC Semantic Ranking (Forge+ and Deep with ccc)
+
+**IF `tools.ccc` is true in forge-tier.yaml:**
+
+Before aggregating extraction results, use CCC to assess semantic significance of changes:
+
+1. Run `ccc_bridge.search("{skill_name}", source_root, top_k=15)` — **Tool resolution:** `/ccc` skill search (Claude Code), ccc MCP (Cursor), `ccc search` (CLI) — to get the skill's most semantically central files
+2. Cross-reference the change manifest files with CCC results
+3. Files appearing in BOTH the change manifest AND CCC's top results are **semantically significant changes** — flag them for priority in the merge step
+4. Store `{ccc_significant_changes: [{file, score}]}` in context
+
+This helps the merge step (section 4) prioritize which changes are most likely to affect the skill's core content vs. peripheral modifications.
+
+CCC failures: skip ranking silently, all changes treated equally.
+
+**Note on remote sources:** If `source_root` is a workspace clone, the CCC index may already exist from a prior forge and can be reused via `ccc search --refresh`. If the source is an ephemeral fallback clone, the clone path is not indexed by CCC — the search will return empty results and semantic ranking will be skipped. Deferred CCC indexing is implemented in create-skill step-03 but not in update-skill. All changes are treated equally for ephemeral remote sources.
+
+**IF `tools.ccc` is false:** Skip this section silently.
+
+### 3. Deep Tier QMD Enrichment (Conditional)
+
+**ONLY if forge_tier == Deep:**
+
+Read the `qmd_collections` registry from `{sidecar_path}/forge-tier.yaml`.
+
+Find the collection entry matching the current skill: look for an entry where `skill_name` matches the skill being updated AND `type` is `"extraction"`.
+
+**If a matching extraction collection is found:**
+Launch a subprocess that loads qmd_bridge and for each changed export:
+1. Queries the `{skill_name}-extraction` collection for semantic context related to the export
+2. Searches for usage patterns, documentation references, temporal history
+3. Returns T2 evidence per export (usage frequency, context snippets, related concepts)
+
+**If no matching collection found in registry:**
+Log: "No QMD extraction collection found for {skill_name}. T2 enrichment skipped. Re-run [CS] Create Skill to generate the collection."
+Continue without T2 enrichment — extraction still produces T1 results.
+
+**If forge_tier != Deep:** Skip this section with notice: "QMD enrichment skipped (tier: {forge_tier})"
+
+### 4. Compile Extraction Results
+
+Aggregate all subprocess results into structured extraction data:
+
+```
+Extraction Results:
+  files_extracted: [count]
+  exports_extracted: [count]
+  confidence_breakdown:
+    T1: [count]
+    T1-low: [count]
+    T2: [count]
+
+  Per-file extractions:
+    {file_path}:
+      exports:
+        - name: {export_name}
+          type: function|class|type|constant
+          signature: {full signature}
+          location: {file}:{start_line}-{end_line}
+          confidence: T1|T1-low|T2
+          parameters: [{name, type}]
+          return_type: {type}
+          docstring: {summary}
+          qmd_evidence: {if Deep tier}
+```
+
+### 5. Display Extraction Summary and Auto-Proceed
+
+"**Re-Extraction Complete:**
+
+| Metric | Count |
+|--------|-------|
+| Files extracted | {count} |
+| Exports extracted | {count} |
+| T1 (AST-verified) | {count} |
+| T1-low (pattern-matched) | {count} |
+| T2 (QMD-enriched) | {count} |
+
+**Proceeding to merge with existing skill...**"
+
+### 6. Present MENU OPTIONS
+
+Display: "**Proceeding to merge...**"
+
+- After extraction results are compiled, immediately load, read entire file, then execute {nextStepFile}
+- This is an auto-proceed step with no user choices
+
+## CRITICAL STEP COMPLETION NOTE
+
+ONLY WHEN all changed files have been extracted and results compiled will you load {nextStepFile} to begin the merge operation.
+

package/src/{workflows/update-skill → skf-update-skill}/steps-c/step-04-merge.md

@@ -1,10 +1,7 @@
 ---
-name: 'step-04-merge'
-description: 'Merge new extractions into existing skill content, preserving all [MANUAL] sections with conflict resolution'
-
 nextStepFile: './step-05-validate.md'
-manualSectionRulesFile: '../data/manual-section-rules.md'
-mergeConflictRulesFile: '../data/merge-conflict-rules.md'
+manualSectionRulesFile: 'references/manual-section-rules.md'
+mergeConflictRulesFile: 'references/merge-conflict-rules.md'
 ---
 
 # Step 4: Merge
@@ -13,45 +10,12 @@ mergeConflictRulesFile: '../data/merge-conflict-rules.md'
 
 Merge freshly extracted export data into the existing SKILL.md content while preserving all [MANUAL] sections. Detect and resolve conflicts where regenerated content overlaps developer-authored content. For stack skills, merge across all output files.
 
-## MANDATORY EXECUTION RULES (READ FIRST):
-
-### Universal Rules:
-
-- 🛑 NEVER generate content without user input
-- 📖 CRITICAL: Read the complete step file before taking any action
-- 🔄 CRITICAL: When loading next step with 'C', ensure entire file is read
-- 📋 YOU ARE A FACILITATOR, not a content generator
-- ⚙️ TOOL/SUBPROCESS FALLBACK: If any instruction references a subprocess, subagent, or tool you do not have access to, you MUST still achieve the outcome in your main context thread
-- ✅ YOU MUST ALWAYS SPEAK OUTPUT in your Agent communication style with the config `{communication_language}`
-
-### Role Reinforcement:
-
-- ✅ You are a precision code analyst operating in Surgeon mode
-- ✅ [MANUAL] section preservation is the HIGHEST PRIORITY — zero content loss
-- ✅ Every merge decision must be traceable and reversible
-- ✅ When in doubt about [MANUAL] conflicts, HALT and ask the user
-
-### Step-Specific Rules:
-
-- 🎯 Focus ONLY on merging extractions into existing skill content
-- 🚫 FORBIDDEN to delete or modify [MANUAL] section content
-- 🚫 FORBIDDEN to write files — merge produces an edit plan for step 06 to execute
-- 💬 If [MANUAL] conflicts detected: HALT and present to user for resolution
-- 💬 If clean merge: auto-proceed without user interaction
-
-## EXECUTION PROTOCOLS:
+## Rules
 
-- 🎯 Follow MANDATORY SEQUENCE exactly
-- 💾 Load merge rules from data files for conflict resolution
-- 📖 Track every merge operation for evidence report
-- 🚫 FORBIDDEN to auto-resolve [MANUAL] conflicts — user must decide
-
-## CONTEXT BOUNDARIES:
-
-- Available: extraction results from step 03, existing SKILL.md content, [MANUAL] inventory from step 01, change manifest from step 02
-- Focus: content merge and [MANUAL] preservation
-- Limits: merge planning only — no file writes (step 06 executes the edit plan)
-- Dependencies: step 03 must have produced extraction results
+- Focus only on merging extractions into existing skill content
+- Never delete or modify [MANUAL] section content
+- Write merged SKILL.md (and stack reference files) directly to disk at section 6b — Claude Code's Edit/Write tools commit on call, so there is no held-in-memory "edit plan" primitive; subsequent steps validate and verify against the on-disk files
+- If [MANUAL] conflicts detected: halt and present to user. If clean merge: auto-proceed
 
 ## MANDATORY SEQUENCE
 
@@ -101,12 +65,37 @@ Follow the merge priority order from {mergeConflictRulesFile}:
 - No conflicts expected (new content, no existing [MANUAL])
 
 **Priority 6 — Process script/asset file changes (from Category D in change manifest):**
-- MODIFIED_FILE: queue file for re-copy from source, update `file_entries` content_hash
-- DELETED_FILE: queue file for removal from `scripts/` or `assets/`, remove from `file_entries`
-- NEW_FILE: queue file for copy from source, add to `file_entries`
-- Files in `scripts/[MANUAL]/` or `assets/[MANUAL]/` are never modified (user-authored)
-- Update Section 7b manifest table to reflect changes
-- Update `metadata.json` `scripts[]`/`assets[]` arrays and `stats.scripts_count`/`stats.assets_count`
+
+Category D operates on every `file_entries[]` row regardless of `file_type`. Handle each entry by its type:
+
+- **`file_type: "script"` or `file_type: "asset"`:**
+  - MODIFIED_FILE: queue file for re-copy from source, update `file_entries` content_hash
+  - DELETED_FILE: queue file for removal from `scripts/` or `assets/`, remove from `file_entries`
+  - NEW_FILE: queue file for copy from source, add to `file_entries`
+  - Files in `scripts/[MANUAL]/` or `assets/[MANUAL]/` are never modified (user-authored)
+  - Update Section 7b manifest table to reflect changes
+  - Update `metadata.json` `scripts[]`/`assets[]` arrays and `stats.scripts_count`/`stats.assets_count`
+
+- **`file_type: "doc"`** (authoritative docs promoted by §2a/§1b):
+  - MODIFIED_FILE: update `file_entries` content_hash only. **Do NOT copy the file** — doc-type entries are source-tracked but not bundled. Record the drift in the update report.
+  - DELETED_FILE: remove from `file_entries`. **Do NOT remove any file from the skill package** (there was nothing copied). Record the removal in the update report — a deleted authoritative doc is a meaningful upstream signal.
+  - NEW_FILE: this path is not used for doc type — new doc entries come from Priority 7 below, not from Category D. If Category D reports NEW_FILE with `file_type: "doc"`, log a warning and route to Priority 7.
+
+**Priority 7 — Process new authoritative docs (from `promoted_docs_new[]` populated by §1b):**
+
+For each entry in the in-context `promoted_docs_new[]` list:
+
+- Add a new row to `file_entries[]` in the merged provenance map with:
+  - `file_name`: `"docs/authoritative/{source_path}"` (synthetic namespace — see skill-sections.md for convention)
+  - `file_type`: `"doc"`
+  - `source_file`: the path from `promoted_docs_new[].path`
+  - `content_hash`: the hash pre-computed by §1b
+  - `confidence`: `"T1-low"`
+  - `extraction_method`: `"promoted-authoritative"`
+- Do NOT copy the file into the skill package (doc type is source-tracked, not bundled).
+- Record in the update report: `"Added authoritative doc: {path} (heuristic: {basename})"`.
+
+**If `promoted_docs_new[]` is empty:** skip Priority 7 silently. No report entry.
 
 ### 4. Check for Conflicts
 
@@ -169,6 +158,27 @@ Merge Results:
   stack_files_merged: [count] (if stack skill)
 ```
 
+### 6b. Write Merged Files to Disk
+
+Write the merged content produced by sections 3–5 directly to disk now. Later steps read from these files for validation and verification. The write must happen exactly once, here.
+
+**Write SKILL.md:**
+- Use the `Edit` or `Write` tool to write merged SKILL.md content to `{skill_package}/SKILL.md`
+- Preserve UTF-8 encoding
+- If the source version detected during step-03 differs from the previous metadata version, create the new `{skill_package}` directory (`{skill_group}/{new_version}/`) first and write there — the previous version's directory is preserved on disk. Update `{skill_package}` in context to point at the new path.
+
+**Write stack reference files (if `skill_type == "stack"`):**
+- For each affected file from section 5, use `Edit` or `Write` to write:
+  - `references/{library}.md` with merged per-library content
+  - `references/integrations/{pair}.md` with merged per-integration content
+- Preserve [MANUAL] blocks exactly as captured in section 2.
+
+**Do NOT write here:**
+- `metadata.json`, `provenance-map.json`, `evidence-report.md` — derived from merge + validation output, written by step-06 sections 2–4
+- `context-snippet.md` — regenerated from the on-disk SKILL.md + metadata.json by step-06 section 5
+
+**Halt-on-tool-failure:** If any `Edit`/`Write` call errors (permission denied, disk full, path invalid, etc.), halt and report the failure — do not proceed to step-05 validation. The skill package may be in a partial state and will need manual recovery before re-running update-skill.
+
 ### 7. Display Merge Summary
 
 "**Merge Complete:**
@@ -195,6 +205,7 @@ Display: "**Merge complete with conflict resolution. Select:** [C] Continue to V
 #### EXECUTION RULES:
 
 - ALWAYS halt and wait for user input after conflict resolution
+- **GATE [default: C if clean merge]** — If `{headless_mode}` and merge is clean (no [MANUAL] conflicts): auto-proceed with [C] Continue, log: "headless: clean merge, auto-continue". If conflicts exist, HALT even in headless mode — conflicts require human judgment.
 - ONLY proceed when user selects 'C'
 
 **If clean merge (no conflicts):**
@@ -213,26 +224,3 @@ Display: "**Clean merge — proceeding to validation...**"
 
 ONLY WHEN all merge operations are complete and any [MANUAL] conflicts have been resolved by the user will you load {nextStepFile} to begin validation.
 
----
-
-## 🚨 SYSTEM SUCCESS/FAILURE METRICS
-
-### ✅ SUCCESS:
-
-- All [MANUAL] sections preserved with zero content loss
-- Merge applied in correct priority order (delete → move → rename → modify → add)
-- Every conflict presented to user for resolution (no auto-resolution of [MANUAL] conflicts)
-- Stack skill files merged if applicable
-- Merge results compiled with full accounting
-- Clean merges auto-proceed; conflict merges require user [C]
-
-### ❌ SYSTEM FAILURE:
-
-- ANY [MANUAL] content lost or modified without user consent
-- Auto-resolving [MANUAL] conflicts without user input
-- Writing files during merge planning (edits are executed in step 06)
-- Applying merge out of priority order
-- Not detecting orphaned [MANUAL] blocks on deleted exports
-- Not handling stack skill multi-file merge
-
-**Master Rule:** Skipping steps, optimizing sequences, or not following exact instructions is FORBIDDEN and constitutes SYSTEM FAILURE.

package/src/{workflows/update-skill → skf-update-skill}/steps-c/step-05-validate.md

@@ -1,7 +1,4 @@
 ---
-name: 'step-05-validate'
-description: 'Validate updated skill against spec, verify MANUAL integrity, and check confidence tier consistency'
-
 nextStepFile: './step-06-write.md'
 ---
 
@@ -11,44 +8,11 @@ nextStepFile: './step-06-write.md'
 
 Validate the merged skill content against the agentskills.io specification, verify all [MANUAL] sections survived the merge intact, and check confidence tier consistency across all re-extracted content. This is an advisory validation — findings are warnings, not blockers.
 
-## MANDATORY EXECUTION RULES (READ FIRST):
-
-### Universal Rules:
-
-- 🛑 NEVER generate content without user input
-- 📖 CRITICAL: Read the complete step file before taking any action
-- 🔄 CRITICAL: When loading next step with 'C', ensure entire file is read
-- 📋 YOU ARE A FACILITATOR, not a content generator
-- ⚙️ TOOL/SUBPROCESS FALLBACK: If any instruction references a subprocess, subagent, or tool you do not have access to, you MUST still achieve the outcome in your main context thread
-- ✅ YOU MUST ALWAYS SPEAK OUTPUT in your Agent communication style with the config `{communication_language}`
-
-### Role Reinforcement:
-
-- ✅ You are a precision code analyst operating in Surgeon mode
-- ✅ Validation is advisory — flag issues but do not block the workflow
-- ✅ Every finding must include specific file:line reference
-- ✅ Zero-hallucination principle applies to validation findings too
-
-### Step-Specific Rules:
-
-- 🎯 Focus ONLY on validation — do not fix issues (that's the user's choice)
-- 🚫 FORBIDDEN to modify merged content — validation is read-only
-- 💬 Launch parallel validation checks when subprocess available (Pattern 4): In Claude Code, use multiple parallel Agent tool calls. In Cursor, use parallel requests (IDE-dependent). In CLI, use `xargs -P`. See [knowledge/tool-resolution.md](../../../knowledge/tool-resolution.md)
-- ⚙️ If subprocess unavailable, perform checks sequentially in main thread
-
-## EXECUTION PROTOCOLS:
-
-- 🎯 Follow MANDATORY SEQUENCE exactly
-- 💾 Compile validation findings with severity levels
-- 📖 Track pass/fail for each validation category
-- 🚫 Validation is ADVISORY — do not block on warnings
+## Rules
 
-## CONTEXT BOUNDARIES:
-
-- Available: merged skill content from step 04, extraction results from step 03, [MANUAL] inventory from step 01
-- Focus: quality assurance — spec compliance, [MANUAL] integrity, confidence consistency
-- Limits: read-only — do not modify merged content
-- Dependencies: step 04 must have completed merge (with or without conflict resolution)
+- Focus only on validation — do not fix issues (that's the user's choice)
+- Validation is read-only — do not modify merged content
+- Use parallel validation checks (Pattern 4) when available; if unavailable, check sequentially
 
 ## MANDATORY SEQUENCE
 
@@ -63,7 +27,7 @@ Run: `npx skill-check -h`
 
 **Important:** Do not assume availability — empirical check required.
 
-**Validation timing note:** Step-04 produces an edit plan, not written files. Checks that require files on disk (skill-check Checks A, E, F) will be **deferred to post-write** — step-06 runs them after writing files. Structural checks (B, C, D) validate the planned merge content and run here.
+**Validation timing note:** Step-04 section 6b has already written SKILL.md (and stack reference files) to disk. External-tool checks against written files (skill-check Checks A, E, F) still run in **step-06 section 7** to co-locate external-tool validation with post-write verification. Structural checks (B, C, D) run here against the merged content — content on disk is byte-identical to the in-context copy.
 
 ### 2. Launch Parallel Validation Checks
 
@@ -156,24 +120,3 @@ After validation summary is displayed, immediately load, read entire file, then
 
 ONLY WHEN all validation checks have completed and findings are displayed will you load {nextStepFile} to write the updated files. Validation does NOT block — it informs.
 
----
-
-## 🚨 SYSTEM SUCCESS/FAILURE METRICS
-
-### ✅ SUCCESS:
-
-- All six checks executed (spec-manual, [MANUAL], confidence, provenance, diff, security)
-- Checks A (spec compliance via skill-check), E (diff), and F (security scan) deferred to post-write in step-06
-- Manual structural check performed for spec compliance in this step
-- Stack skill reference files validated if applicable
-- Findings reported with severity and specific locations; [MANUAL] integrity verified
-- Auto-proceeds regardless of findings (advisory mode)
-
-### ❌ SYSTEM FAILURE:
-
-- Skipping any of the six checks; blocking on validation warnings
-- Not verifying [MANUAL] integrity; hallucinating findings not backed by comparison
-- Modifying merged content during validation (validation is read-only in this step)
-- Not recording quality score when skill-check is available
-
-**Master Rule:** Skipping steps, optimizing sequences, or not following exact instructions is FORBIDDEN and constitutes SYSTEM FAILURE.