milens 0.7.1 → 0.7.2

package/.agents/skills/adapters/SKILL.md

@@ -1,8 +1,10 @@
 ---
+generated-by: milens
 name: milens-adapters
 description: Code intelligence for the adapters area — symbols, dependencies, and entry points
 ---
 
+<!-- Generated by milens — safe to delete/regenerate -->
 # Adapters
 
 ## Working with this area
@@ -25,8 +27,11 @@ When working with code in **adapters/**, follow these mandatory safety rules:
 | Text search across files | `mcp_milens_grep` |
 | See file symbols | `mcp_milens_get_file_symbols` |
 
+### Edit-safety enforcement
+A `PreToolUse` hook (warn mode by default) reminds you if no milens safety check (`impact`/`context`/`overview`/`guard_edit_check`/`edit_check`/`smart_context`) was called before an `Edit`/`Write`/`MultiEdit`. Opt-in strict deny mode is available via `milens hooks guard-set-mode --mode strict`. Both modes consume the check after one edit. See `.milens/hook-state/config.json`. Known caveat: the underlying `PreToolUse` deny mechanism has at least one reliability issue (https://github.com/anthropics/claude-code/issues/4362).
+
 ## Overview
-Contains 60 symbols (54 exported) across 6 files.
+Contains 61 symbols (55 exported) across 6 files.
 
 ## Key Symbols
 - **`Milens Adapter Packs`** [section] (adapters/README.md:1) — 0 refs
@@ -34,16 +39,16 @@ Contains 60 symbols (54 exported) across 6 files.
 - **`Available Adapters`** [section] (adapters/README.md:9) — 0 refs
 - **`Installation`** [section] (adapters/README.md:21) — 0 refs
 - **`Claude Code`** [section] (adapters/README.md:23) — 0 refs
-- **`OpenCode`** [section] (adapters/README.md:54) — 0 refs
-- **`Codex`** [section] (adapters/README.md:61) — 0 refs
-- **`Cursor`** [section] (adapters/README.md:67) — 0 refs
-- **`GitHub Copilot`** [section] (adapters/README.md:74) — 0 refs
-- **`Gemini`** [section] (adapters/README.md:81) — 0 refs
-- **`Zed`** [section] (adapters/README.md:87) — 0 refs
-- **`Verification`** [section] (adapters/README.md:93) — 0 refs
-- **`Index Maintenance`** [section] (adapters/README.md:101) — 0 refs
-- **`All Tools Available`** [section] (adapters/README.md:109) — 0 refs
-- **`Safety Rules (applies to all harnesses)`** [section] (adapters/README.md:127) — 0 refs
+- **`Claude Code — via `/plugin install` (marketplace)`** [section] (adapters/README.md:50) — 0 refs
+- **`OpenCode`** [section] (adapters/README.md:65) — 0 refs
+- **`Codex`** [section] (adapters/README.md:72) — 0 refs
+- **`Cursor`** [section] (adapters/README.md:78) — 0 refs
+- **`GitHub Copilot`** [section] (adapters/README.md:85) — 0 refs
+- **`Gemini`** [section] (adapters/README.md:92) — 0 refs
+- **`Zed`** [section] (adapters/README.md:98) — 0 refs
+- **`Verification`** [section] (adapters/README.md:104) — 0 refs
+- **`Index Maintenance`** [section] (adapters/README.md:112) — 0 refs
+- **`All Tools Available`** [section] (adapters/README.md:120) — 0 refs
 
 ## Files
 - adapters/README.md

package/.agents/skills/analyzer/SKILL.md

@@ -1,8 +1,10 @@
 ---
+generated-by: milens
 name: milens-analyzer
 description: Code intelligence for the analyzer area — symbols, dependencies, and entry points
 ---
 
+<!-- Generated by milens — safe to delete/regenerate -->
 # Analyzer
 
 ## Working with this area
@@ -25,16 +27,19 @@ When working with code in **analyzer/**, follow these mandatory safety rules:
 | Text search across files | `mcp_milens_grep` |
 | See file symbols | `mcp_milens_get_file_symbols` |
 
+### Edit-safety enforcement
+A `PreToolUse` hook (warn mode by default) reminds you if no milens safety check (`impact`/`context`/`overview`/`guard_edit_check`/`edit_check`/`smart_context`) was called before an `Edit`/`Write`/`MultiEdit`. Opt-in strict deny mode is available via `milens hooks guard-set-mode --mode strict`. Both modes consume the check after one edit. See `.milens/hook-state/config.json`. Known caveat: the underlying `PreToolUse` deny mechanism has at least one reliability issue (https://github.com/anthropics/claude-code/issues/4362).
+
 ## Overview
-Contains 119 symbols (24 exported) across 8 files.
+Contains 131 symbols (24 exported) across 8 files.
 
 ## Key Symbols
 - **`analyze`** [function] (src/analyzer/engine.ts:139) — 10 refs
-- **`resolveLinksWithStats`** [function] (src/analyzer/resolver.ts:37) — 9 refs
-- **`reviewPr`** [function] (src/analyzer/review.ts:244) — 9 refs
+- **`resolveLinksWithStats`** [function] (src/analyzer/resolver.ts:54) — 9 refs
+- **`reviewPr`** [function] (src/analyzer/review.ts:261) — 9 refs
 - **`countDependentFiles`** [function] (src/analyzer/risk.ts:13) — 9 refs
 - **`loadAliases`** [function] (src/analyzer/config.ts:10) — 6 refs
-- **`ResolutionResult`** [interface] (src/analyzer/resolver.ts:24) — 6 refs
+- **`ResolutionResult`** [interface] (src/analyzer/resolver.ts:39) — 6 refs
 - **`classifyRisk`** [function] (src/analyzer/risk.ts:33) — 5 refs
 - **`scoreSymbolRisk`** [function] (src/analyzer/risk.ts:41) — 5 refs
 - **`diffResolutions`** [function] (src/analyzer/scope-resolver.ts:768) — 5 refs
@@ -43,7 +48,7 @@ Contains 119 symbols (24 exported) across 8 files.
 - **`scanFiles`** [function] (src/analyzer/scanner.ts:11) — 4 refs
 - **`resolveWithScopes`** [function] (src/analyzer/scope-resolver.ts:48) — 4 refs
 - **`clearTreeCache`** [function] (src/analyzer/engine.ts:29) — 3 refs
-- **`resolveLinks`** [function] (src/analyzer/resolver.ts:32) — 3 refs
+- **`resolveLinks`** [function] (src/analyzer/resolver.ts:49) — 3 refs
 
 ## Entry Points
 - **`ScopeNode`** [interface] — 11 incoming references
@@ -54,7 +59,7 @@ Contains 119 symbols (24 exported) across 8 files.
 
 ## Dependencies
 - **parser**: `langForFile`, `supportedExtensions`, `getParser`, `loadLanguage`, `extractFromTree`, `clearQueryCache`, `extractVueScript`, `extractVueTemplateRefs` (+9 more)
-- **root**: `isTestFile`, `CodeSymbol`, `ExtractionResult`, `RawImport`, `RawCall`, `RawHeritage`, `RawReExport`, `RawTypeBinding` (+7 more)
+- **root**: `isTestFile`, `CodeSymbol`, `ExtractionResult`, `RawImport`, `RawCall`, `RawHeritage`, `RawReExport`, `RawTypeBinding` (+8 more)
 - **store**: `Database`, `TfIdfProvider`, `EmbeddingStore`, `buildEmbeddingText`, `isFileUpToDate`, `upsertFileHash`, `getSymbolsByFile`, `transaction` (+18 more)
 - **ui**: `ProgressPhase`, `ProgressReporter`, `startPhase`, `tick`, `endPhase`, `finalize`
 

package/.agents/skills/apps/SKILL.md

@@ -1,8 +1,10 @@
 ---
+generated-by: milens
 name: milens-apps
 description: Code intelligence for the apps area — symbols, dependencies, and entry points
 ---
 
+<!-- Generated by milens — safe to delete/regenerate -->
 # Apps
 
 ## Working with this area
@@ -25,6 +27,9 @@ When working with code in **apps/**, follow these mandatory safety rules:
 | Text search across files | `mcp_milens_grep` |
 | See file symbols | `mcp_milens_get_file_symbols` |
 
+### Edit-safety enforcement
+A `PreToolUse` hook (warn mode by default) reminds you if no milens safety check (`impact`/`context`/`overview`/`guard_edit_check`/`edit_check`/`smart_context`) was called before an `Edit`/`Write`/`MultiEdit`. Opt-in strict deny mode is available via `milens hooks guard-set-mode --mode strict`. Both modes consume the check after one edit. See `.milens/hook-state/config.json`. Known caveat: the underlying `PreToolUse` deny mechanism has at least one reliability issue (https://github.com/anthropics/claude-code/issues/4362).
+
 ## Overview
 Contains 40 symbols (8 exported) across 6 files.
 
@@ -40,10 +45,10 @@ Contains 40 symbols (8 exported) across 6 files.
 
 ## Entry Points
 - **`DASHBOARD_URL`** [variable] — 3 incoming references
+- **`serverProcess`** [variable] — 3 incoming references
 - **`loadOverview`** [function] — 2 incoming references
 - **`poll`** [function] — 2 incoming references
 - **`__dirname`** [variable] — 2 incoming references
-- **`setStatus`** [function] — 1 incoming references
 
 ## Dependencies
 - **store**: `remove`, `getAnnotations`, `Database`, `getCodebaseSummary`

package/.agents/skills/docs/SKILL.md

@@ -1,8 +1,10 @@
 ---
+generated-by: milens
 name: milens-docs
 description: Code intelligence for the docs area — symbols, dependencies, and entry points
 ---
 
+<!-- Generated by milens — safe to delete/regenerate -->
 # Docs
 
 ## Working with this area
@@ -25,6 +27,9 @@ When working with code in **docs/**, follow these mandatory safety rules:
 | Text search across files | `mcp_milens_grep` |
 | See file symbols | `mcp_milens_get_file_symbols` |
 
+### Edit-safety enforcement
+A `PreToolUse` hook (warn mode by default) reminds you if no milens safety check (`impact`/`context`/`overview`/`guard_edit_check`/`edit_check`/`smart_context`) was called before an `Edit`/`Write`/`MultiEdit`. Opt-in strict deny mode is available via `milens hooks guard-set-mode --mode strict`. Both modes consume the check after one edit. See `.milens/hook-state/config.json`. Known caveat: the underlying `PreToolUse` deny mechanism has at least one reliability issue (https://github.com/anthropics/claude-code/issues/4362).
+
 ## Overview
 Contains 122 symbols (112 exported) across 10 files.
 
@@ -43,7 +48,7 @@ Contains 122 symbols (112 exported) across 10 files.
 - **`Available Adapters`** [section] (docs/adapters.md:5) — 0 refs
 - **`Quick Install`** [section] (docs/adapters.md:17) — 0 refs
 - **`Claude Code`** [section] (docs/adapters.md:21) — 0 refs
-- **`OpenCode`** [section] (docs/adapters.md:37) — 0 refs
+- **`OpenCode`** [section] (docs/adapters.md:39) — 0 refs
 
 ## Files
 - docs/README.md

package/.agents/skills/milens/SKILL.md

@@ -1,4 +1,5 @@
 ---
+generated-by: milens
 name: milens
 description: Code intelligence MCP tools — symbol search, text grep, impact analysis, dependency graph
 ---
@@ -6,7 +7,7 @@ description: Code intelligence MCP tools — symbol search, text grep, impact an
 <!-- milens:start -->
 # Milens — AI-DOS
 
-The Operating System for AI-Driven Development. This project is indexed by milens (2264 symbols, 2936 links, 229 files).
+The Operating System for AI-Driven Development. This project is indexed by milens (2362 symbols, 3127 links, 235 files).
 
 > **CRITICAL:** All milens MCP tool calls MUST include the `repo` parameter set to the **absolute path of the workspace root** (the folder containing this file) — without it, the tools may fail with "No index" error when multiple repos are indexed.
 
@@ -229,13 +230,14 @@ Milens indexes **Markdown files** (.md, .mdx) — headings become `section` symb
 
 ## Reference
 
-### ⭐ Core Tools — Use Every Session (8)
+### ⭐ Core Tools — Use Every Session (9)
 
 | Tool | Purpose |
 |---|---|
 | `mcp_milens_overview` | **Use this first.** Combined context + impact + grep. 1 call replaces 3-5 file reads. |
 | `mcp_milens_impact` | Blast radius BEFORE editing. Shows what WILL BREAK. |
 | `mcp_milens_edit_check` | Pre-edit safety: callers + exports + re-export chains + test coverage |
+| `mcp_milens_guard_edit_check` | HARD pre-edit gate: blocks if dependents > 5, tracks checks for session audit |
 | `mcp_milens_context` | 360° view: all callers + all callees. Instant dependency graph. |
 | `mcp_milens_query` | Find symbol definitions by name (FTS5 instant search) |
 | `mcp_milens_grep` | Search ALL files for any text (templates, configs, docs, styles) |
@@ -262,10 +264,11 @@ Milens indexes **Markdown files** (.md, .mdx) — headings become `section` symb
 | `mcp_milens_find_dead_code` | Unused exported symbols | Before major refactors |
 | `mcp_milens_find_similar` | Symbols with shared callers/callees | Finding refactor patterns |
 
-### 📚 Advanced Tools — Reference (19)
+### 📚 Advanced Tools — Reference (20)
 
 | Tool | Purpose |
 |---|---|
+| `mcp_milens_generate_findings_report` | Render investigated findings into a Markdown+XML report for a worker/coder agent |
 | `mcp_milens_status` | Index health: symbols, links, files, coverage, staleness |
 | `mcp_milens_repos` | List all indexed repositories |
 | `mcp_milens_annotate` | Record observations about symbols (persists across sessions) |

package/.agents/skills/orchestrator/SKILL.md

@@ -1,8 +1,10 @@
 ---
+generated-by: milens
 name: milens-orchestrator
 description: Code intelligence for the orchestrator area — symbols, dependencies, and entry points
 ---
 
+<!-- Generated by milens — safe to delete/regenerate -->
 # Orchestrator
 
 ## Working with this area
@@ -25,6 +27,9 @@ When working with code in **orchestrator/**, follow these mandatory safety rules
 | Text search across files | `mcp_milens_grep` |
 | See file symbols | `mcp_milens_get_file_symbols` |
 
+### Edit-safety enforcement
+A `PreToolUse` hook (warn mode by default) reminds you if no milens safety check (`impact`/`context`/`overview`/`guard_edit_check`/`edit_check`/`smart_context`) was called before an `Edit`/`Write`/`MultiEdit`. Opt-in strict deny mode is available via `milens hooks guard-set-mode --mode strict`. Both modes consume the check after one edit. See `.milens/hook-state/config.json`. Known caveat: the underlying `PreToolUse` deny mechanism has at least one reliability issue (https://github.com/anthropics/claude-code/issues/4362).
+
 ## Overview
 Contains 23 symbols (7 exported) across 2 files.
 

package/.agents/skills/parser/SKILL.md

@@ -1,8 +1,10 @@
 ---
+generated-by: milens
 name: milens-parser
 description: Code intelligence for the parser area — symbols, dependencies, and entry points
 ---
 
+<!-- Generated by milens — safe to delete/regenerate -->
 # Parser
 
 ## Working with this area
@@ -25,24 +27,27 @@ When working with code in **parser/**, follow these mandatory safety rules:
 | Text search across files | `mcp_milens_grep` |
 | See file symbols | `mcp_milens_get_file_symbols` |
 
+### Edit-safety enforcement
+A `PreToolUse` hook (warn mode by default) reminds you if no milens safety check (`impact`/`context`/`overview`/`guard_edit_check`/`edit_check`/`smart_context`) was called before an `Edit`/`Write`/`MultiEdit`. Opt-in strict deny mode is available via `milens hooks guard-set-mode --mode strict`. Both modes consume the check after one edit. See `.milens/hook-state/config.json`. Known caveat: the underlying `PreToolUse` deny mechanism has at least one reliability issue (https://github.com/anthropics/claude-code/issues/4362).
+
 ## Overview
-Contains 82 symbols (31 exported) across 16 files.
+Contains 85 symbols (31 exported) across 16 files.
 
 ## Key Symbols
 - **`LangSpec`** [interface] (src/parser/extract.ts:6) — 32 refs
 - **`loadLanguage`** [function] (src/parser/loader.ts:21) — 15 refs
 - **`getParser`** [function] (src/parser/loader.ts:32) — 14 refs
-- **`extractFromTree`** [function] (src/parser/extract.ts:267) — 9 refs
+- **`extractFromTree`** [function] (src/parser/extract.ts:274) — 9 refs
 - **`supportedExtensions`** [function] (src/parser/languages.ts:29) — 6 refs
 - **`extractHtmlScripts`** [function] (src/parser/lang-html.ts:38) — 5 refs
 - **`extractMarkdown`** [function] (src/parser/lang-md.ts:34) — 5 refs
-- **`spec`** [variable] (src/parser/lang-ts.ts:5) — 5 refs
+- **`spec`** [variable] (src/parser/lang-ts.ts:1) — 5 refs
 - **`extractVueScript`** [function] (src/parser/lang-vue.ts:19) — 5 refs
 - **`initTreeSitter`** [function] (src/parser/loader.ts:15) — 5 refs
-- **`clearQueryCache`** [function] (src/parser/extract.ts:72) — 4 refs
+- **`clearQueryCache`** [function] (src/parser/extract.ts:79) — 4 refs
 - **`extractHtmlRefs`** [function] (src/parser/lang-html.ts:57) — 4 refs
 - **`extractHtmlLinks`** [function] (src/parser/lang-html.ts:99) — 4 refs
-- **`spec`** [variable] (src/parser/lang-js.ts:5) — 4 refs
+- **`spec`** [variable] (src/parser/lang-js.ts:1) — 4 refs
 - **`extractVueTemplateRefs`** [function] (src/parser/lang-vue.ts:38) — 4 refs
 
 ## Entry Points
@@ -53,7 +58,7 @@ Contains 82 symbols (31 exported) across 16 files.
 - **`supportedExtensions`** [function] — 6 incoming references
 
 ## Dependencies
-- **root**: `CodeSymbol`, `RawImport`, `RawCall`, `RawHeritage`, `RawReExport`, `RawTypeBinding`, `RawAssignmentBinding`, `RawReturnType` (+3 more)
+- **root**: `CodeSymbol`, `RawImport`, `RawCall`, `RawHeritage`, `RawReExport`, `RawTypeBinding`, `RawAssignmentBinding`, `RawReturnType` (+4 more)
 - **analyzer**: `resolve`
 - **store**: `load`
 

package/.agents/skills/root/SKILL.md

@@ -1,8 +1,10 @@
 ---
+generated-by: milens
 name: milens-root
 description: Code intelligence for the root area — symbols, dependencies, and entry points
 ---
 
+<!-- Generated by milens — safe to delete/regenerate -->
 # Root
 
 ## Working with this area
@@ -25,30 +27,33 @@ When working with code in **root/**, follow these mandatory safety rules:
 | Text search across files | `mcp_milens_grep` |
 | See file symbols | `mcp_milens_get_file_symbols` |
 
+### Edit-safety enforcement
+A `PreToolUse` hook (warn mode by default) reminds you if no milens safety check (`impact`/`context`/`overview`/`guard_edit_check`/`edit_check`/`smart_context`) was called before an `Edit`/`Write`/`MultiEdit`. Opt-in strict deny mode is available via `milens hooks guard-set-mode --mode strict`. Both modes consume the check after one edit. See `.milens/hook-state/config.json`. Known caveat: the underlying `PreToolUse` deny mechanism has at least one reliability issue (https://github.com/anthropics/claude-code/issues/4362).
+
 ## Overview
-Contains 236 symbols (156 exported) across 12 files.
+Contains 238 symbols (157 exported) across 12 files.
 
 ## Key Symbols
-- **`CodeSymbol`** [interface] (src/types.ts:8) — 50 refs
+- **`CodeSymbol`** [interface] (src/types.ts:8) — 52 refs
 - **`SymbolLink`** [interface] (src/types.ts:26) — 22 refs
-- **`RawCall`** [interface] (src/types.ts:45) — 15 refs
-- **`isTestFile`** [function] (src/utils.ts:2) — 10 refs
+- **`RawCall`** [interface] (src/types.ts:45) — 18 refs
+- **`isTestFile`** [function] (src/utils.ts:4) — 10 refs
 - **`RawImport`** [interface] (src/types.ts:35) — 9 refs
 - **`RawHeritage`** [interface] (src/types.ts:59) — 7 refs
 - **`ExtractionResult`** [interface] (src/types.ts:67) — 6 refs
-- **`RawTypeBinding`** [interface] (src/types.ts:87) — 6 refs
-- **`RawAssignmentBinding`** [interface] (src/types.ts:95) — 6 refs
-- **`globToRegex`** [function] (src/utils.ts:11) — 6 refs
-- **`RawReturnType`** [interface] (src/types.ts:103) — 5 refs
-- **`RawCallResultBinding`** [interface] (src/types.ts:111) — 5 refs
-- **`AnalysisStats`** [interface] (src/types.ts:120) — 5 refs
+- **`RawTypeBinding`** [interface] (src/types.ts:88) — 6 refs
+- **`RawAssignmentBinding`** [interface] (src/types.ts:96) — 6 refs
+- **`globToRegex`** [function] (src/utils.ts:16) — 6 refs
+- **`RawReturnType`** [interface] (src/types.ts:104) — 5 refs
+- **`RawCallResultBinding`** [interface] (src/types.ts:112) — 5 refs
+- **`AnalysisStats`** [interface] (src/types.ts:135) — 5 refs
 - **`generateAgentsMd`** [function] (src/agents-md.ts:93) — 4 refs
 - **`computeMetrics`** [function] (src/metrics.ts:21) — 4 refs
 
 ## Entry Points
-- **`CodeSymbol`** [interface] — 50 incoming references
+- **`CodeSymbol`** [interface] — 52 incoming references
 - **`SymbolLink`** [interface] — 22 incoming references
-- **`RawCall`** [interface] — 15 incoming references
+- **`RawCall`** [interface] — 18 incoming references
 - **`isTestFile`** [function] — 10 incoming references
 - **`RawImport`** [interface] — 9 incoming references
 
@@ -56,18 +61,18 @@ Contains 236 symbols (156 exported) across 12 files.
 - **store**: `Database`, `RepoRegistry`, `AnnotationStore`, `runDecayPass`, `getIncomingLinks`, `getAllSymbols`, `getCodebaseSummary`, `findDbPath` (+22 more)
 - **analyzer**: `loadAliases`, `analyze`, `resolve`
 - **ui**: `createProgressReporter`, `finalize`
-- **server**: `startHttp`, `startStdio`, `HookManager`, `defaultOnSessionStart`, `defaultOnSessionEnd`, `defaultOnPreCompact`, `defaultOnPostCompact`, `enableHook` (+3 more)
+- **server**: `startHttp`, `startStdio`, `HookManager`, `defaultOnSessionStart`, `defaultOnSessionEnd`, `defaultOnPreCompact`, `defaultOnPostCompact`, `handleMarkChecked` (+6 more)
 - **security**: `loadRules`, `auditDependencies`
 - **orchestrator**: `Orchestrator`, `subscribe`, `runAndFormat`
 
 ## Used By
-- **analyzer**: `isTestFile`, `CodeSymbol`, `ExtractionResult`, `RawImport`, `RawCall`, `RawHeritage`, `RawReExport`, `RawTypeBinding` (+7 more)
+- **analyzer**: `isTestFile`, `CodeSymbol`, `ExtractionResult`, `RawImport`, `RawCall`, `RawHeritage`, `RawReExport`, `RawTypeBinding` (+8 more)
 - **orchestrator**: `CodeSymbol`
-- **parser**: `CodeSymbol`, `RawImport`, `RawCall`, `RawHeritage`, `RawReExport`, `RawTypeBinding`, `RawAssignmentBinding`, `RawReturnType` (+3 more)
+- **parser**: `CodeSymbol`, `RawImport`, `RawCall`, `RawHeritage`, `RawReExport`, `RawTypeBinding`, `RawAssignmentBinding`, `RawReturnType` (+4 more)
 - **server**: `generateCrossRefSection`, `globToRegex`
 - **store**: `Annotation`, `AnnotationKey`, `Session`, `EvolutionEvent`, `CodeSymbol`, `SymbolLink`, `RepoEntry`
 - **ui**: `AnalysisStats`
-- **test**: `generateAgentsMd`, `AnnotationKey`, `CodeSymbol`, `SymbolLink`, `computeMetrics`, `formatMetricsReport`, `MilensMetrics`, `RawImport` (+17 more)
+- **test**: `generateAgentsMd`, `AnnotationKey`, `CodeSymbol`, `SymbolLink`, `computeMetrics`, `formatMetricsReport`, `MilensMetrics`, `RawImport` (+18 more)
 
 ## Files
 - AGENTS.md

package/.agents/skills/scripts/SKILL.md

@@ -1,8 +1,10 @@
 ---
+generated-by: milens
 name: milens-scripts
 description: Code intelligence for the scripts area — symbols, dependencies, and entry points
 ---
 
+<!-- Generated by milens — safe to delete/regenerate -->
 # Scripts
 
 ## Working with this area
@@ -25,22 +27,24 @@ When working with code in **scripts/**, follow these mandatory safety rules:
 | Text search across files | `mcp_milens_grep` |
 | See file symbols | `mcp_milens_get_file_symbols` |
 
+### Edit-safety enforcement
+A `PreToolUse` hook (warn mode by default) reminds you if no milens safety check (`impact`/`context`/`overview`/`guard_edit_check`/`edit_check`/`smart_context`) was called before an `Edit`/`Write`/`MultiEdit`. Opt-in strict deny mode is available via `milens hooks guard-set-mode --mode strict`. Both modes consume the check after one edit. See `.milens/hook-state/config.json`. Known caveat: the underlying `PreToolUse` deny mechanism has at least one reliability issue (https://github.com/anthropics/claude-code/issues/4362).
+
 ## Overview
-Contains 77 symbols (0 exported) across 6 files.
+Contains 80 symbols (0 exported) across 7 files.
 
 ## Entry Points
 - **`ghApi`** [function] — 4 incoming references
-- **`detectBreakingFromLabels`** [function] — 4 incoming references
 - **`exec`** [function] — 3 incoming references
 - **`branch`** [variable] — 3 incoming references
-- **`detectTypeFromBranch`** [function] — 3 incoming references
+- **`detectBreakingFromLabels`** [function] — 3 incoming references
+- **`fail`** [function] — 3 incoming references
 
 ## Dependencies
 - **analyzer**: `resolve`
 
 ## Used By
 - **apps**: `parseArgs`, `generatePrPayload`
-- **test**: `detectTypeFromBranch`, `detectScopeFromBranch`, `detectBreakingFromBranch`, `detectBreakingFromLabels`, `slugify`, `parseArgs`, `generateTitle`, `generateBody` (+1 more)
 
 ## Files
 - scripts/build-standalone.mjs
@@ -49,3 +53,4 @@ Contains 77 symbols (0 exported) across 6 files.
 - scripts/gen-build-info.mjs
 - scripts/pr-generator.cjs
 - scripts/smoke-test.mjs
+- scripts/sync-version.mjs

package/.agents/skills/security/SKILL.md

@@ -1,8 +1,10 @@
 ---
+generated-by: milens
 name: milens-security
 description: Code intelligence for the security area — symbols, dependencies, and entry points
 ---
 
+<!-- Generated by milens — safe to delete/regenerate -->
 # Security
 
 ## Working with this area
@@ -25,25 +27,28 @@ When working with code in **security/**, follow these mandatory safety rules:
 | Text search across files | `mcp_milens_grep` |
 | See file symbols | `mcp_milens_get_file_symbols` |
 
+### Edit-safety enforcement
+A `PreToolUse` hook (warn mode by default) reminds you if no milens safety check (`impact`/`context`/`overview`/`guard_edit_check`/`edit_check`/`smart_context`) was called before an `Edit`/`Write`/`MultiEdit`. Opt-in strict deny mode is available via `milens hooks guard-set-mode --mode strict`. Both modes consume the check after one edit. See `.milens/hook-state/config.json`. Known caveat: the underlying `PreToolUse` deny mechanism has at least one reliability issue (https://github.com/anthropics/claude-code/issues/4362).
+
 ## Overview
-Contains 45 symbols (15 exported) across 2 files.
+Contains 47 symbols (17 exported) across 2 files.
 
 ## Key Symbols
-- **`loadRules`** [function] (src/security/rules.ts:1302) — 6 refs
+- **`loadRules`** [function] (src/security/rules.ts:1301) — 6 refs
 - **`auditDependencies`** [function] (src/security/deps.ts:732) — 4 refs
 - **`detectEcosystem`** [function] (src/security/deps.ts:512) — 3 refs
 - **`parseDependencies`** [function] (src/security/deps.ts:524) — 3 refs
 - **`checkVulnerabilities`** [function] (src/security/deps.ts:687) — 3 refs
 - **`Ecosystem`** [type] (src/security/deps.ts:8) — 3 refs
+- **`ALL_RULES`** [variable] (src/security/rules.ts:99) — 3 refs
 - **`VulnerabilityReport`** [interface] (src/security/deps.ts:26) — 2 refs
-- **`getRulesByCategory`** [function] (src/security/rules.ts:1309) — 2 refs
-- **`getRulesBySeverity`** [function] (src/security/rules.ts:1313) — 2 refs
+- **`getRulesByCategory`** [function] (src/security/rules.ts:1308) — 2 refs
+- **`getRulesBySeverity`** [function] (src/security/rules.ts:1312) — 2 refs
 - **`SecurityCategory`** [type] (src/security/rules.ts:3) — 1 refs
 - **`Dependency`** [interface] (src/security/deps.ts:10) — 0 refs
 - **`Vulnerability`** [interface] (src/security/deps.ts:16) — 0 refs
 - **`SecurityRule`** [interface] (src/security/rules.ts:31) — 0 refs
 - **`SecurityMatch`** [interface] (src/security/rules.ts:47) — 0 refs
-- **`SecurityReport`** [interface] (src/security/rules.ts:59) — 0 refs
 
 ## Entry Points
 - **`readManifest`** [function] — 6 incoming references

package/.agents/skills/server/SKILL.md

@@ -1,8 +1,10 @@
 ---
+generated-by: milens
 name: milens-server
 description: Code intelligence for the server area — symbols, dependencies, and entry points
 ---
 
+<!-- Generated by milens — safe to delete/regenerate -->
 # Server
 
 ## Working with this area
@@ -25,35 +27,38 @@ When working with code in **server/**, follow these mandatory safety rules:
 | Text search across files | `mcp_milens_grep` |
 | See file symbols | `mcp_milens_get_file_symbols` |
 
+### Edit-safety enforcement
+A `PreToolUse` hook (warn mode by default) reminds you if no milens safety check (`impact`/`context`/`overview`/`guard_edit_check`/`edit_check`/`smart_context`) was called before an `Edit`/`Write`/`MultiEdit`. Opt-in strict deny mode is available via `milens hooks guard-set-mode --mode strict`. Both modes consume the check after one edit. See `.milens/hook-state/config.json`. Known caveat: the underlying `PreToolUse` deny mechanism has at least one reliability issue (https://github.com/anthropics/claude-code/issues/4362).
+
 ## Overview
-Contains 113 symbols (22 exported) across 10 files.
+Contains 154 symbols (37 exported) across 12 files.
 
 ## Key Symbols
+- **`Deps`** [interface] (src/server/tools/deps.ts:4) — 11 refs
 - **`HookManager`** [class] (src/server/hooks.ts:43) — 9 refs
-- **`Deps`** [interface] (src/server/tools/deps.ts:4) — 9 refs
 - **`defaultOnSessionStart`** [function] (src/server/hooks.ts:100) — 8 refs
 - **`defaultOnSessionEnd`** [function] (src/server/hooks.ts:174) — 8 refs
 - **`defaultOnPreCompact`** [function] (src/server/hooks.ts:350) — 8 refs
 - **`defaultOnPostCompact`** [function] (src/server/hooks.ts:368) — 8 refs
+- **`createMcpServer`** [function] (src/server/mcp.ts:452) — 6 refs
 - **`HookConfig`** [interface] (src/server/hooks.ts:5) — 5 refs
 - **`FileWatcher`** [class] (src/server/watcher.ts:50) — 5 refs
+- **`readMode`** [function] (src/server/guard-hook.ts:38) — 4 refs
+- **`writeMode`** [function] (src/server/guard-hook.ts:50) — 4 refs
+- **`handleMarkChecked`** [function] (src/server/guard-hook.ts:147) — 4 refs
+- **`handleCheckEdit`** [function] (src/server/guard-hook.ts:161) — 4 refs
 - **`defaultOnPreCommit`** [function] (src/server/hooks.ts:237) — 4 refs
 - **`defaultOnFileChange`** [function] (src/server/hooks.ts:323) — 4 refs
-- **`SessionContext`** [interface] (src/server/hooks.ts:15) — 4 refs
-- **`registerAllPrompts`** [function] (src/server/mcp-prompts.ts:623) — 4 refs
-- **`createMcpServer`** [function] (src/server/mcp.ts:452) — 4 refs
-- **`startStdio`** [function] (src/server/mcp.ts:2306) — 4 refs
-- **`startHttp`** [function] (src/server/mcp.ts:2363) — 4 refs
 
 ## Entry Points
+- **`Deps`** [interface] — 11 incoming references
 - **`HookManager`** [class] — 9 incoming references
-- **`Deps`** [interface] — 9 incoming references
 - **`defaultOnSessionStart`** [function] — 8 incoming references
 - **`defaultOnSessionEnd`** [function] — 8 incoming references
 - **`defaultOnPreCompact`** [function] — 8 incoming references
 
 ## Dependencies
-- **store**: `Database`, `AnnotationStore`, `RepoRegistry`, `runDecayPass`, `getCodebaseSummary`, `recall`, `getStats`, `getTestCoverage` (+36 more)
+- **store**: `Database`, `AnnotationStore`, `RepoRegistry`, `runDecayPass`, `getCodebaseSummary`, `recall`, `getStats`, `getTestCoverage` (+38 more)
 - **root**: `generateCrossRefSection`, `globToRegex`
 - **analyzer**: `reviewPr`, `countDependentFiles`, `analyze`
 - **parser**: `getParser`, `loadLanguage`, `ALL_LANGS`
@@ -61,15 +66,17 @@ Contains 113 symbols (22 exported) across 10 files.
 - **security**: `loadRules`
 
 ## Used By
-- **root**: `startHttp`, `startStdio`, `HookManager`, `defaultOnSessionStart`, `defaultOnSessionEnd`, `defaultOnPreCompact`, `defaultOnPostCompact`, `enableHook` (+3 more)
-- **test**: `defaultOnSessionStart`, `defaultOnPreCompact`, `defaultOnSessionEnd`, `defaultOnPostCompact`, `HookManager`, `HookConfig`, `defaultOnPreCommit`, `defaultOnFileChange` (+19 more)
+- **root**: `startHttp`, `startStdio`, `HookManager`, `defaultOnSessionStart`, `defaultOnSessionEnd`, `defaultOnPreCompact`, `defaultOnPostCompact`, `handleMarkChecked` (+6 more)
+- **test**: `defaultOnSessionStart`, `defaultOnPreCompact`, `defaultOnSessionEnd`, `defaultOnPostCompact`, `createMcpServer`, `markChecked`, `checkEdit`, `readMode` (+26 more)
 
 ## Files
+- src/server/guard-hook.ts
 - src/server/hooks.ts
 - src/server/mcp-prompts.ts
 - src/server/mcp.ts
 - src/server/test-plan.ts
 - src/server/tools/deps.ts
+- src/server/tools/findings-report.ts
 - src/server/tools/resources.ts
 - src/server/tools/security.ts
 - src/server/tools/session.ts

package/.agents/skills/store/SKILL.md

@@ -1,8 +1,10 @@
 ---
+generated-by: milens
 name: milens-store
 description: Code intelligence for the store area — symbols, dependencies, and entry points
 ---
 
+<!-- Generated by milens — safe to delete/regenerate -->
 # Store
 
 ## Working with this area
@@ -25,13 +27,16 @@ When working with code in **store/**, follow these mandatory safety rules:
 | Text search across files | `mcp_milens_grep` |
 | See file symbols | `mcp_milens_get_file_symbols` |
 
+### Edit-safety enforcement
+A `PreToolUse` hook (warn mode by default) reminds you if no milens safety check (`impact`/`context`/`overview`/`guard_edit_check`/`edit_check`/`smart_context`) was called before an `Edit`/`Write`/`MultiEdit`. Opt-in strict deny mode is available via `milens hooks guard-set-mode --mode strict`. Both modes consume the check after one edit. See `.milens/hook-state/config.json`. Known caveat: the underlying `PreToolUse` deny mechanism has at least one reliability issue (https://github.com/anthropics/claude-code/issues/4362).
+
 ## Overview
-Contains 139 symbols (15 exported) across 5 files.
+Contains 146 symbols (15 exported) across 5 files.
 
 ## Key Symbols
 - **`Database`** [class] (src/store/db.ts:10) — 80 refs
 - **`AnnotationStore`** [class] (src/store/annotations.ts:10) — 21 refs
-- **`RepoRegistry`** [class] (src/store/registry.ts:18) — 16 refs
+- **`RepoRegistry`** [class] (src/store/registry.ts:24) — 18 refs
 - **`runDecayPass`** [function] (src/store/confidence.ts:87) — 6 refs
 - **`buildEmbeddingText`** [function] (src/store/vectors.ts:250) — 4 refs
 - **`TfIdfProvider`** [class] (src/store/vectors.ts:44) — 4 refs
@@ -48,8 +53,8 @@ Contains 139 symbols (15 exported) across 5 files.
 ## Entry Points
 - **`Database`** [class] — 80 incoming references
 - **`AnnotationStore`** [class] — 21 incoming references
-- **`RepoRegistry`** [class] — 16 incoming references
-- **`findSymbolById`** [method] — 14 incoming references
+- **`RepoRegistry`** [class] — 18 incoming references
+- **`findSymbolById`** [method] — 15 incoming references
 - **`rowToSymbol`** [function] — 13 incoming references
 
 ## Dependencies
@@ -59,7 +64,7 @@ Contains 139 symbols (15 exported) across 5 files.
 - **root**: `Database`, `RepoRegistry`, `AnnotationStore`, `runDecayPass`, `getIncomingLinks`, `getAllSymbols`, `getCodebaseSummary`, `findDbPath` (+22 more)
 - **analyzer**: `Database`, `TfIdfProvider`, `EmbeddingStore`, `buildEmbeddingText`, `isFileUpToDate`, `upsertFileHash`, `getSymbolsByFile`, `transaction` (+18 more)
 - **orchestrator**: `Database`, `findSymbolByName`, `findUpstream`, `getTestCoverageGaps`, `findDeadCode`
-- **server**: `Database`, `AnnotationStore`, `RepoRegistry`, `runDecayPass`, `getCodebaseSummary`, `recall`, `getStats`, `getTestCoverage` (+36 more)
+- **server**: `Database`, `AnnotationStore`, `RepoRegistry`, `runDecayPass`, `getCodebaseSummary`, `recall`, `getStats`, `getTestCoverage` (+38 more)
 - **test**: `Database`, `AnnotationStore`, `RepoRegistry`, `boostConfidence`, `decayConfidence`, `getStaleAnnotations`, `promoteSecurityAnnotations`, `runDecayPass` (+76 more)
 - **apps**: `remove`, `getAnnotations`, `Database`, `getCodebaseSummary`
 - **parser**: `load`