milens 0.6.3 → 0.6.5

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

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+---
+name: milens-tdd
+description: Test-Driven Development with Code Intelligence — find gaps, generate test plans, implement, and verify
+---
+
+# milens-tdd — Test-Driven Development with Code Intelligence
+
+Identify untested symbols ranked by risk, generate targeted test strategies, implement tests, and verify coverage.
+
+## Tools Required
+
+| Tool | Purpose |
+|---|---|
+| `mcp_milens_test_coverage_gaps` | Find untested symbols sorted by risk |
+| `mcp_milens_test_plan` | Generate mock strategy and test scenarios for a symbol |
+| `mcp_milens_test_impact` | Identify affected test files after changes |
+| `mcp_milens_review_pr` | Post-change quality check for CRITICAL issues |
+
+> **CRITICAL:** All milens MCP tool calls MUST include the `repo` parameter set to the **absolute path of the workspace root**.
+
+## Workflow
+
+### Step 1: Identify Untested Symbols
+
+Start by finding symbols with no test coverage, sorted by risk (hotspots first).
+
+```
+mcp_milens_test_coverage_gaps({repo: "<workspaceRoot>", limit: 10})
+```
+
+Review the output:
+- **HIGH risk symbols** — complex logic, high fan-in, many dependents. Prioritize these.
+- **MEDIUM risk symbols** — moderate complexity, some dependents.
+- **LOW risk symbols** — simple getters, one-liners. Lowest priority.
+
+### Step 2: Generate Test Plans
+
+For each high-risk symbol identified in Step 1, request a test plan.
+
+```
+mcp_milens_test_plan({name: "<symbolName>", repo: "<workspaceRoot>"})
+```
+
+The test plan provides:
+- **Mock strategy** — what to stub, what to isolate
+- **3+ test scenarios** — happy path, edge cases, error states
+- **Setup requirements** — dependencies to initialize
+- **Expected assertions** — what each test should verify
+
+### Step 3: Implement Tests
+
+Write test files based on the test plan output:
+
+1. Check if test files already exist for the module
+2. Follow existing test patterns in the codebase (frameworks, conventions, helper utilities)
+3. Implement each test scenario from the plan
+4. Keep tests focused — one behavior per test
+
+### Step 4: Verify Test Impact
+
+After writing tests, confirm which test files changed and should run.
+
+```
+mcp_milens_test_impact({repo: "<workspaceRoot>"})
+```
+
+This lists all test files affected by the current changes. Run those tests to validate.
+
+### Step 5: Quality Check
+
+Run the PR review to catch any CRITICAL issues before committing.
+
+```
+mcp_milens_review_pr({repo: "<workspaceRoot>"})
+```
+
+Address any CRITICAL or HIGH findings before completing the cycle.
+
+## Example Session
+
+### Input
+
+```
+"add tests for the resolveLinks function"
+```
+
+### Tool Calls
+
+**Step 1 — Find gaps:**
+```
+mcp_milens_test_coverage_gaps({repo: "/home/user/project", limit: 10})
+```
+
+**Output:**
+```
+Coverage Gaps (untested exported symbols):
+1. resolveLinks [function] — HIGH risk (12 dependents, 8 callers)
+2. parseConfig [function] — MEDIUM risk (5 dependents)
+3. formatOutput [function] — LOW risk (1 dependent)
+...
+```
+
+**Step 2 — Test plan for high-risk:**
+```
+mcp_milens_test_plan({name: "resolveLinks", repo: "/home/user/project"})
+```
+
+**Output:**
+```
+Test Plan for resolveLinks:
+  Mock strategy: stub loadAliases, stub database queries
+  Tests:
+    1. resolves direct links between two symbols
+    2. handles circular dependency chain gracefully
+    3. returns empty array when no links found
+    4. throws on malformed symbol data
+  Setup: import SymbolLink from '@/types', mock store layer
+```
+
+**Step 3 — Implement tests** in `src/__tests__/resolver.test.ts`
+
+**Step 4 — Verify:**
+```
+mcp_milens_test_impact({repo: "/home/user/project"})
+```
+
+**Output:**
+```
+Affected test files:
+  src/__tests__/resolver.test.ts (new)
+  src/__tests__/analyzer.test.ts (modified, re-export impact)
+```
+
+**Step 5 — Quality:**
+```
+mcp_milens_review_pr({repo: "/home/user/project"})
+```
+
+**Output:** No CRITICAL issues. 2 LOW suggestions.
+
+## Best Practices
+
+1. **Prioritize by risk, not alphabetically.** A HIGH-risk utility with 50 callers matters more than a LOW-risk getter nobody uses.
+2. **Don't test implementation details.** Follow the test plan's mock strategy — stub at module boundaries, not internal functions.
+3. **One behavior per test.** Each test should verify a single scenario (happy path, edge case, error) with a descriptive name.
+4. **Verify before commit.** Always run Step 4 (`test_impact`) and Step 5 (`review_pr`) before merging. Don't skip the quality gate.
+5. **Re-check gaps after large refactors.** A refactor can move symbols from "tested" back to "untested."
+
+## Quality Gate
+
+| Criteria | Pass | Fail |
+|---|---|---|
+| Test coverage gaps | HIGH-risk symbols have tests | HIGH-risk symbols still uncovered after session |
+| Test plan adherence | ≥3 scenarios implemented per symbol | Tests don't match plan scenarios |
+| Test impact verification | All affected test files pass | Any test file fails |
+| PR review | No CRITICAL issues | Unresolved CRITICAL issues remain |

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

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+---
+name: milens-orchestrator
+description: Code intelligence for the orchestrator area — symbols, dependencies, and entry points
+---
+
+# Orchestrator
+
+## Working with this area
+When working with code in **orchestrator/**, follow these mandatory safety rules:
+
+### Before editing any symbol in this area:
+1. Call `mcp_milens_impact({target: "<symbol>", repo: "<workspaceRoot>"})` — check blast radius
+2. If depth-1 dependents > 5 → **STOP and warn** before proceeding
+3. Call `mcp_milens_context({name: "<symbol>", repo: "<workspaceRoot>"})` — see all callers/callees
+
+### Before committing changes in this area:
+1. Call `mcp_milens_detect_changes({repo: "<workspaceRoot>"})` — verify scope
+2. If unexpected files changed → **STOP and report**
+
+### Key tools for this area:
+| Task | Tool |
+|---|---|
+| Find all references | `mcp_milens_context` |
+| Check edit safety | `mcp_milens_edit_check` |
+| Text search across files | `mcp_milens_grep` |
+| See file symbols | `mcp_milens_get_file_symbols` |
+
+## Overview
+Contains 22 symbols (7 exported) across 2 files.
+
+## Key Symbols
+- **`Orchestrator`** [class] (src/orchestrator/orchestrator.ts:36) — 6 refs
+- **`OrchestratorReport`** [interface] (src/orchestrator/reporter.ts:4) — 5 refs
+- **`formatReport`** [function] (src/orchestrator/reporter.ts:17) — 4 refs
+- **`OrchestratorConfig`** [interface] (src/orchestrator/orchestrator.ts:10) — 2 refs
+- **`ImpactSnapshot`** [interface] (src/orchestrator/orchestrator.ts:18) — 2 refs
+- **`ReportOptions`** [interface] (src/orchestrator/reporter.ts:13) — 2 refs
+- **`ImpactDiff`** [interface] (src/orchestrator/orchestrator.ts:25) — 1 refs
+
+## Entry Points
+- **`Orchestrator`** [class] — 6 incoming references
+- **`OrchestratorReport`** [interface] — 5 incoming references
+- **`formatReport`** [function] — 4 incoming references
+- **`snapshot`** [method] — 3 incoming references
+- **`run`** [method] — 3 incoming references
+
+## Dependencies
+- **store**: `Database`, `findSymbolByName`, `findUpstream`, `clear`, `getTestCoverageGaps`, `findDeadCode`, `close`
+- **analyzer**: `reviewPr`, `ReviewResult`, `SymbolRisk`
+- **root**: `CodeSymbol`, `has`
+
+## Used By
+- **root**: `Orchestrator`, `subscribe`, `runAndFormat`
+- **server**: `Orchestrator`, `snapshot`, `compare`, `runAndFormat`
+- **test**: `Orchestrator`, `formatReport`, `OrchestratorReport`, `subscribe`, `run`, `snapshot`, `compare`, `cancel` (+3 more)
+
+## Files
+- src/orchestrator/orchestrator.ts
+- src/orchestrator/reporter.ts

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

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+---
+name: milens-parser
+description: Code intelligence for the parser area — symbols, dependencies, and entry points
+---
+
+# Parser
+
+## Working with this area
+When working with code in **parser/**, follow these mandatory safety rules:
+
+### Before editing any symbol in this area:
+1. Call `mcp_milens_impact({target: "<symbol>", repo: "<workspaceRoot>"})` — check blast radius
+2. If depth-1 dependents > 5 → **STOP and warn** before proceeding
+3. Call `mcp_milens_context({name: "<symbol>", repo: "<workspaceRoot>"})` — see all callers/callees
+
+### Before committing changes in this area:
+1. Call `mcp_milens_detect_changes({repo: "<workspaceRoot>"})` — verify scope
+2. If unexpected files changed → **STOP and report**
+
+### Key tools for this area:
+| Task | Tool |
+|---|---|
+| Find all references | `mcp_milens_context` |
+| Check edit safety | `mcp_milens_edit_check` |
+| Text search across files | `mcp_milens_grep` |
+| See file symbols | `mcp_milens_get_file_symbols` |
+
+## Overview
+Contains 76 symbols (26 exported) across 15 files.
+
+## Key Symbols
+- **`LangSpec`** [interface] (src/parser/extract.ts:6) — 30 refs
+- **`loadLanguage`** [function] (src/parser/loader.ts:21) — 14 refs
+- **`getParser`** [function] (src/parser/loader.ts:32) — 13 refs
+- **`extractFromTree`** [function] (src/parser/extract.ts:250) — 8 refs
+- **`supportedExtensions`** [function] (src/parser/languages.ts:29) — 6 refs
+- **`extractHtmlScripts`** [function] (src/parser/lang-html.ts:33) — 5 refs
+- **`extractMarkdown`** [function] (src/parser/lang-md.ts:34) — 5 refs
+- **`spec`** [variable] (src/parser/lang-ts.ts:5) — 5 refs
+- **`extractVueScript`** [function] (src/parser/lang-vue.ts:18) — 5 refs
+- **`initTreeSitter`** [function] (src/parser/loader.ts:15) — 5 refs
+- **`clearQueryCache`** [function] (src/parser/extract.ts:67) — 4 refs
+- **`extractHtmlRefs`** [function] (src/parser/lang-html.ts:52) — 4 refs
+- **`extractVueTemplateRefs`** [function] (src/parser/lang-vue.ts:37) — 4 refs
+- **`langForFile`** [function] (src/parser/languages.ts:24) — 4 refs
+- **`spec`** [variable] (src/parser/lang-js.ts:5) — 3 refs
+
+## Entry Points
+- **`LangSpec`** [interface] — 30 incoming references
+- **`loadLanguage`** [function] — 14 incoming references
+- **`getParser`** [function] — 13 incoming references
+- **`extractFromTree`** [function] — 8 incoming references
+- **`supportedExtensions`** [function] — 6 incoming references
+
+## Dependencies
+- **root**: `CodeSymbol`, `RawImport`, `RawCall`, `RawHeritage`, `RawReExport`, `RawTypeBinding`, `RawAssignmentBinding`, `RawReturnType` (+4 more)
+- **test**: `lang`, `parser`
+- **analyzer**: `find`, `resolve`
+- **store**: `load`
+
+## Used By
+- **analyzer**: `langForFile`, `supportedExtensions`, `getParser`, `loadLanguage`, `extractFromTree`, `clearQueryCache`, `extractVueScript`, `extractVueTemplateRefs` (+6 more)
+- **server**: `getParser`, `loadLanguage`, `ALL_LANGS`
+- **test**: `getParser`, `loadLanguage`, `extractFromTree`, `extractVueScript`, `extractVueTemplateRefs`, `spec`, `extractHtmlScripts`, `extractHtmlRefs` (+7 more)
+
+## Files
+- src/parser/extract.ts
+- src/parser/lang-css.ts
+- src/parser/lang-go.ts
+- src/parser/lang-html.ts
+- src/parser/lang-java.ts
+- src/parser/lang-js.ts
+- src/parser/lang-md.ts
+- src/parser/lang-php.ts
+- src/parser/lang-py.ts
+- src/parser/lang-ruby.ts
+- src/parser/lang-rust.ts
+- src/parser/lang-ts.ts
+- src/parser/lang-vue.ts
+- src/parser/languages.ts
+- src/parser/loader.ts

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

@@ -0,0 +1,86 @@
+---
+name: milens-root
+description: Code intelligence for the root area — symbols, dependencies, and entry points
+---
+
+# Root
+
+## Working with this area
+When working with code in **root/**, follow these mandatory safety rules:
+
+### Before editing any symbol in this area:
+1. Call `mcp_milens_impact({target: "<symbol>", repo: "<workspaceRoot>"})` — check blast radius
+2. If depth-1 dependents > 5 → **STOP and warn** before proceeding
+3. Call `mcp_milens_context({name: "<symbol>", repo: "<workspaceRoot>"})` — see all callers/callees
+
+### Before committing changes in this area:
+1. Call `mcp_milens_detect_changes({repo: "<workspaceRoot>"})` — verify scope
+2. If unexpected files changed → **STOP and report**
+
+### Key tools for this area:
+| Task | Tool |
+|---|---|
+| Find all references | `mcp_milens_context` |
+| Check edit safety | `mcp_milens_edit_check` |
+| Text search across files | `mcp_milens_grep` |
+| See file symbols | `mcp_milens_get_file_symbols` |
+
+## Overview
+Contains 198 symbols (147 exported) across 13 files.
+
+## Key Symbols
+- **`CodeSymbol`** [interface] (src/types.ts:8) — 41 refs
+- **`SymbolLink`** [interface] (src/types.ts:26) — 21 refs
+- **`isTestFile`** [function] (src/utils.ts:2) — 11 refs
+- **`RawCall`** [interface] (src/types.ts:44) — 7 refs
+- **`RawImport`** [interface] (src/types.ts:35) — 6 refs
+- **`ExtractionResult`** [interface] (src/types.ts:60) — 6 refs
+- **`generateAgentsMd`** [function] (src/agents-md.ts:43) — 4 refs
+- **`computeMetrics`** [function] (src/metrics.ts:21) — 4 refs
+- **`formatMetricsReport`** [function] (src/metrics.ts:62) — 4 refs
+- **`MilensMetrics`** [interface] (src/metrics.ts:4) — 4 refs
+- **`generateSkills`** [function] (src/skills.ts:19) — 4 refs
+- **`RawHeritage`** [interface] (src/types.ts:52) — 4 refs
+- **`RawTypeBinding`** [interface] (src/types.ts:80) — 4 refs
+- **`RawAssignmentBinding`** [interface] (src/types.ts:88) — 4 refs
+- **`RawReturnType`** [interface] (src/types.ts:96) — 4 refs
+
+## Entry Points
+- **`CodeSymbol`** [interface] — 41 incoming references
+- **`has`** [function] — 29 incoming references
+- **`SymbolLink`** [interface] — 21 incoming references
+- **`isTestFile`** [function] — 11 incoming references
+- **`RawCall`** [interface] — 7 incoming references
+
+## Dependencies
+- **store**: `Database`, `RepoRegistry`, `AnnotationStore`, `runDecayPass`, `getIncomingLinks`, `getAllSymbols`, `getCodebaseSummary`, `register` (+25 more)
+- **analyzer**: `loadAliases`, `analyze`, `resolve`, `clear`
+- **server**: `startHttp`, `startStdio`, `HookManager`, `get`, `enableHook`, `loadConfig`, `saveConfig`, `disableHook`
+- **security**: `loadRules`, `auditDependencies`
+- **orchestrator**: `Orchestrator`, `subscribe`, `runAndFormat`
+- **scripts**: `outDir`
+- **test**: `dbPath`
+
+## Used By
+- **analyzer**: `isTestFile`, `CodeSymbol`, `ExtractionResult`, `RawImport`, `RawCall`, `RawHeritage`, `RawReExport`, `RawTypeBinding` (+8 more)
+- **orchestrator**: `CodeSymbol`, `has`
+- **parser**: `CodeSymbol`, `RawImport`, `RawCall`, `RawHeritage`, `RawReExport`, `RawTypeBinding`, `RawAssignmentBinding`, `RawReturnType` (+4 more)
+- **store**: `Annotation`, `AnnotationKey`, `Session`, `EvolutionEvent`, `CodeSymbol`, `SymbolLink`, `RepoEntry`, `has` (+1 more)
+- **test**: `generateAgentsMd`, `AnnotationKey`, `CodeSymbol`, `SymbolLink`, `computeMetrics`, `formatMetricsReport`, `MilensMetrics`, `RawImport` (+9 more)
+- **security**: `has`
+- **server**: `has`
+
+## Files
+- AGENTS.md
+- CLAUDE.md
+- CONTRIBUTING.md
+- DEPLOY.md
+- README.md
+- milens-generate-skills-issue.md
+- src/agents-md.ts
+- src/cli.ts
+- src/metrics.ts
+- src/skills.ts
+- src/types.ts
+- src/utils.ts
+- vitest.config.ts

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

@@ -0,0 +1,45 @@
+---
+name: milens-scripts
+description: Code intelligence for the scripts area — symbols, dependencies, and entry points
+---
+
+# Scripts
+
+## Working with this area
+When working with code in **scripts/**, follow these mandatory safety rules:
+
+### Before editing any symbol in this area:
+1. Call `mcp_milens_impact({target: "<symbol>", repo: "<workspaceRoot>"})` — check blast radius
+2. If depth-1 dependents > 5 → **STOP and warn** before proceeding
+3. Call `mcp_milens_context({name: "<symbol>", repo: "<workspaceRoot>"})` — see all callers/callees
+
+### Before committing changes in this area:
+1. Call `mcp_milens_detect_changes({repo: "<workspaceRoot>"})` — verify scope
+2. If unexpected files changed → **STOP and report**
+
+### Key tools for this area:
+| Task | Tool |
+|---|---|
+| Find all references | `mcp_milens_context` |
+| Check edit safety | `mcp_milens_edit_check` |
+| Text search across files | `mcp_milens_grep` |
+| See file symbols | `mcp_milens_get_file_symbols` |
+
+## Overview
+Contains 29 symbols (0 exported) across 1 files.
+
+## Entry Points
+- **`ROOT`** [variable] — 2 incoming references
+- **`outDir`** [variable] — 2 incoming references
+- **`resolveTargets`** [function] — 1 incoming references
+- **`run`** [function] — 1 incoming references
+- **`__dirname`** [variable] — 1 incoming references
+
+## Dependencies
+- **analyzer**: `resolve`
+
+## Used By
+- **root**: `outDir`
+
+## Files
+- scripts/build-standalone.mjs

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

@@ -0,0 +1,65 @@
+---
+name: milens-security
+description: Code intelligence for the security area — symbols, dependencies, and entry points
+---
+
+# Security
+
+## Working with this area
+When working with code in **security/**, follow these mandatory safety rules:
+
+### Before editing any symbol in this area:
+1. Call `mcp_milens_impact({target: "<symbol>", repo: "<workspaceRoot>"})` — check blast radius
+2. If depth-1 dependents > 5 → **STOP and warn** before proceeding
+3. Call `mcp_milens_context({name: "<symbol>", repo: "<workspaceRoot>"})` — see all callers/callees
+
+### Before committing changes in this area:
+1. Call `mcp_milens_detect_changes({repo: "<workspaceRoot>"})` — verify scope
+2. If unexpected files changed → **STOP and report**
+
+### Key tools for this area:
+| Task | Tool |
+|---|---|
+| Find all references | `mcp_milens_context` |
+| Check edit safety | `mcp_milens_edit_check` |
+| Text search across files | `mcp_milens_grep` |
+| See file symbols | `mcp_milens_get_file_symbols` |
+
+## Overview
+Contains 35 symbols (15 exported) across 2 files.
+
+## Key Symbols
+- **`loadRules`** [function] (src/security/rules.ts:1044) — 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
+- **`VulnerabilityReport`** [interface] (src/security/deps.ts:26) — 2 refs
+- **`getRulesByCategory`** [function] (src/security/rules.ts:1051) — 2 refs
+- **`getRulesBySeverity`** [function] (src/security/rules.ts:1055) — 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:14) — 0 refs
+- **`SecurityMatch`** [interface] (src/security/rules.ts:29) — 0 refs
+- **`SecurityReport`** [interface] (src/security/rules.ts:41) — 0 refs
+
+## Entry Points
+- **`readManifest`** [function] — 6 incoming references
+- **`loadRules`** [function] — 6 incoming references
+- **`auditDependencies`** [function] — 4 incoming references
+- **`detectEcosystem`** [function] — 3 incoming references
+- **`parseDependencies`** [function] — 3 incoming references
+
+## Dependencies
+- **root**: `has`
+
+## Used By
+- **root**: `loadRules`, `auditDependencies`
+- **server**: `loadRules`
+- **test**: `detectEcosystem`, `parseDependencies`, `checkVulnerabilities`, `auditDependencies`, `loadRules`, `getRulesByCategory`, `getRulesBySeverity`
+
+## Files
+- src/security/deps.ts
+- src/security/rules.ts

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

@@ -0,0 +1,72 @@
+---
+name: milens-server
+description: Code intelligence for the server area — symbols, dependencies, and entry points
+---
+
+# Server
+
+## Working with this area
+When working with code in **server/**, follow these mandatory safety rules:
+
+### Before editing any symbol in this area:
+1. Call `mcp_milens_impact({target: "<symbol>", repo: "<workspaceRoot>"})` — check blast radius
+2. If depth-1 dependents > 5 → **STOP and warn** before proceeding
+3. Call `mcp_milens_context({name: "<symbol>", repo: "<workspaceRoot>"})` — see all callers/callees
+
+### Before committing changes in this area:
+1. Call `mcp_milens_detect_changes({repo: "<workspaceRoot>"})` — verify scope
+2. If unexpected files changed → **STOP and report**
+
+### Key tools for this area:
+| Task | Tool |
+|---|---|
+| Find all references | `mcp_milens_context` |
+| Check edit safety | `mcp_milens_edit_check` |
+| Text search across files | `mcp_milens_grep` |
+| See file symbols | `mcp_milens_get_file_symbols` |
+
+## Overview
+Contains 81 symbols (15 exported) across 4 files.
+
+## Key Symbols
+- **`HookManager`** [class] (src/server/hooks.ts:43) — 6 refs
+- **`HookConfig`** [interface] (src/server/hooks.ts:5) — 5 refs
+- **`defaultOnSessionStart`** [function] (src/server/hooks.ts:100) — 4 refs
+- **`defaultOnSessionEnd`** [function] (src/server/hooks.ts:164) — 4 refs
+- **`defaultOnPreCommit`** [function] (src/server/hooks.ts:227) — 4 refs
+- **`defaultOnFileChange`** [function] (src/server/hooks.ts:313) — 4 refs
+- **`defaultOnPreCompact`** [function] (src/server/hooks.ts:340) — 4 refs
+- **`defaultOnPostCompact`** [function] (src/server/hooks.ts:358) — 4 refs
+- **`SessionContext`** [interface] (src/server/hooks.ts:15) — 4 refs
+- **`registerAllPrompts`** [function] (src/server/mcp-prompts.ts:637) — 4 refs
+- **`createMcpServer`** [function] (src/server/mcp.ts:369) — 4 refs
+- **`generateTestPlan`** [function] (src/server/test-plan.ts:14) — 4 refs
+- **`startStdio`** [function] (src/server/mcp.ts:2716) — 2 refs
+- **`startHttp`** [function] (src/server/mcp.ts:2724) — 2 refs
+- **`TestPlan`** [interface] (src/server/test-plan.ts:3) — 1 refs
+
+## Entry Points
+- **`get`** [method] — 9 incoming references
+- **`HookManager`** [class] — 6 incoming references
+- **`loadConfig`** [method] — 5 incoming references
+- **`HookConfig`** [interface] — 5 incoming references
+- **`defaultOnSessionStart`** [function] — 4 incoming references
+
+## Dependencies
+- **store**: `Database`, `AnnotationStore`, `RepoRegistry`, `runDecayPass`, `getCodebaseSummary`, `recall`, `close`, `getStats` (+37 more)
+- **analyzer**: `reviewPr`, `resolve`, `find`
+- **parser**: `getParser`, `loadLanguage`, `ALL_LANGS`
+- **security**: `loadRules`
+- **orchestrator**: `Orchestrator`, `snapshot`, `compare`, `runAndFormat`
+- **root**: `has`
+- **test**: `dbPath`
+
+## Used By
+- **root**: `startHttp`, `startStdio`, `HookManager`, `get`, `enableHook`, `loadConfig`, `saveConfig`, `disableHook`
+- **test**: `HookManager`, `HookConfig`, `defaultOnSessionStart`, `defaultOnSessionEnd`, `defaultOnPreCommit`, `defaultOnFileChange`, `defaultOnPreCompact`, `defaultOnPostCompact` (+10 more)
+
+## Files
+- src/server/hooks.ts
+- src/server/mcp-prompts.ts
+- src/server/mcp.ts
+- src/server/test-plan.ts

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

@@ -0,0 +1,75 @@
+---
+name: milens-store
+description: Code intelligence for the store area — symbols, dependencies, and entry points
+---
+
+# Store
+
+## Working with this area
+When working with code in **store/**, follow these mandatory safety rules:
+
+### Before editing any symbol in this area:
+1. Call `mcp_milens_impact({target: "<symbol>", repo: "<workspaceRoot>"})` — check blast radius
+2. If depth-1 dependents > 5 → **STOP and warn** before proceeding
+3. Call `mcp_milens_context({name: "<symbol>", repo: "<workspaceRoot>"})` — see all callers/callees
+
+### Before committing changes in this area:
+1. Call `mcp_milens_detect_changes({repo: "<workspaceRoot>"})` — verify scope
+2. If unexpected files changed → **STOP and report**
+
+### Key tools for this area:
+| Task | Tool |
+|---|---|
+| Find all references | `mcp_milens_context` |
+| Check edit safety | `mcp_milens_edit_check` |
+| Text search across files | `mcp_milens_grep` |
+| See file symbols | `mcp_milens_get_file_symbols` |
+
+## Overview
+Contains 135 symbols (15 exported) across 5 files.
+
+## Key Symbols
+- **`Database`** [class] (src/store/db.ts:10) — 77 refs
+- **`AnnotationStore`** [class] (src/store/annotations.ts:10) — 19 refs
+- **`RepoRegistry`** [class] (src/store/registry.ts:18) — 9 refs
+- **`runDecayPass`** [function] (src/store/confidence.ts:85) — 6 refs
+- **`buildEmbeddingText`** [function] (src/store/vectors.ts:250) — 4 refs
+- **`TfIdfProvider`** [class] (src/store/vectors.ts:44) — 4 refs
+- **`EmbeddingStore`** [class] (src/store/vectors.ts:170) — 4 refs
+- **`decayConfidence`** [function] (src/store/confidence.ts:22) — 3 refs
+- **`boostConfidence`** [function] (src/store/confidence.ts:6) — 2 refs
+- **`getStaleAnnotations`** [function] (src/store/confidence.ts:38) — 2 refs
+- **`promoteSecurityAnnotations`** [function] (src/store/confidence.ts:48) — 2 refs
+- **`autoPromote`** [function] (src/store/confidence.ts:106) — 2 refs
+- **`EmbeddingProvider`** [interface] (src/store/vectors.ts:15) — 2 refs
+- **`NeuralProvider`** [class] (src/store/vectors.ts:122) — 0 refs
+- **`SimilarResult`** [interface] (src/store/vectors.ts:23) — 0 refs
+
+## Entry Points
+- **`Database`** [class] — 77 incoming references
+- **`close`** [method] — 29 incoming references
+- **`get`** [method] — 22 incoming references
+- **`AnnotationStore`** [class] — 19 incoming references
+- **`rowToSymbol`** [function] — 13 incoming references
+
+## Dependencies
+- **root**: `Annotation`, `AnnotationKey`, `Session`, `EvolutionEvent`, `CodeSymbol`, `SymbolLink`, `RepoEntry`, `has` (+1 more)
+- **analyzer**: `find`, `resolve`
+- **test**: `dbPath`
+
+## Used By
+- **root**: `Database`, `RepoRegistry`, `AnnotationStore`, `runDecayPass`, `getIncomingLinks`, `getAllSymbols`, `getCodebaseSummary`, `register` (+25 more)
+- **analyzer**: `Database`, `TfIdfProvider`, `EmbeddingStore`, `buildEmbeddingText`, `get`, `clearFiles`, `clear`, `isFileUpToDate` (+23 more)
+- **orchestrator**: `Database`, `findSymbolByName`, `findUpstream`, `clear`, `getTestCoverageGaps`, `findDeadCode`, `close`
+- **server**: `Database`, `AnnotationStore`, `RepoRegistry`, `runDecayPass`, `getCodebaseSummary`, `recall`, `close`, `getStats` (+37 more)
+- **test**: `Database`, `AnnotationStore`, `RepoRegistry`, `boostConfidence`, `decayConfidence`, `getStaleAnnotations`, `promoteSecurityAnnotations`, `runDecayPass` (+76 more)
+- **apps**: `remove`, `Database`, `getCodebaseSummary`, `close`
+- **docs**: `remove`
+- **parser**: `load`
+
+## Files
+- src/store/annotations.ts
+- src/store/confidence.ts
+- src/store/db.ts
+- src/store/registry.ts
+- src/store/vectors.ts