milens 0.6.7 → 0.6.9

package/README.md

@@ -9,8 +9,8 @@
   <a href="https://github.com/fuze210699/milens/blob/main/LICENSE"><img src="https://img.shields.io/badge/license-MIT-blue" alt="license"></a>
   <img src="https://img.shields.io/badge/tools-43-purple" alt="43 tools">
   <img src="https://img.shields.io/badge/languages-12-blue" alt="12 languages">
-  <img src="https://img.shields.io/badge/prompts-7-orange" alt="7 prompts">
-  <img src="https://img.shields.io/badge/security-50%2B-red" alt="50+ rules">
+  <img src="https://img.shields.io/badge/prompts-6-orange" alt="6 prompts">
+  <img src="https://img.shields.io/badge/security-190%2B-red" alt="190+ rules">
   <img src="https://img.shields.io/badge/harnesses-7-lightgrey" alt="7 harnesses">
 </p>
 
@@ -88,14 +88,19 @@ That single command analyzes your codebase, builds a knowledge graph, generates
 
 Then connect your editor:
 
+**Prerequisite:** Install milens globally on your machine:
+```bash
+npm install -g milens      # one-time setup
+```
+
 ```json
 // .vscode/mcp.json — VS Code / Copilot
 {
   "servers": {
     "milens": {
       "type": "stdio",
-      "command": "npx",
-      "args": ["-y", "milens", "serve", "-p", "${workspaceFolder}"]
+      "command": "milens",
+      "args": ["serve", "-p", "${workspaceFolder}"]
     }
   }
 }
@@ -103,7 +108,7 @@ Then connect your editor:
 
 ```bash
 # Claude Code
-claude mcp add milens -- npx -y milens serve -p .
+claude mcp add milens -- milens serve -p .
 ```
 
 <details>
@@ -111,21 +116,21 @@ claude mcp add milens -- npx -y milens serve -p .
 
 ```bash
 # Cursor — .cursor/mcp.json
-{ "mcpServers": { "milens": { "command": "npx", "args": ["-y", "milens", "serve", "-p", "."] } } }
+{ "mcpServers": { "milens": { "command": "milens", "args": ["serve", "-p", "${workspaceFolder}"] } } }
 
-# OpenCode — .opencode/config.json
-{ "mcp": { "milens": { "command": "npx", "args": ["-y", "milens", "serve"] } } }
+# OpenCode — opencode.json
+{ "mcp": { "milens": { "type": "local", "command": ["milens", "serve", "-p", "."] } } }
 
 # Codex — .codex/config.toml
 [mcp_servers.milens]
-command = "npx"
-args = ["-y", "milens", "serve", "-p", "."]
+command = "milens"
+args = ["serve", "-p", "."]
 
 # Gemini — .gemini/settings.json
-{ "mcpServers": { "milens": { "command": "npx", "args": ["-y", "milens", "serve", "-p", "."] } } }
+{ "mcpServers": { "milens": { "command": "milens", "args": ["serve", "-p", "${workspaceFolder}"] } } }
 
 # Zed — .zed/settings.json
-{ "mcp_servers": { "milens": { "command": "npx", "args": ["-y", "milens", "serve", "-p", "."] } } }
+{ "context_servers": { "milens": { "command": "milens serve -p ." } } }
 ```
 
 </details>
@@ -159,7 +164,7 @@ Open your AI agent. It auto-loads `AGENTS.md` with codebase context. You're read
 |---|---|
 | **Code Intelligence** | 43 MCP tools — search, impact, context, trace, routes |
 | **Security Scanner** | 50+ rules across 9 categories + dependency audit |
-| **Sub-Agent Prompts** | 7 prompts — plan, review, tdd, security, architect, debug, dead_code_remove |
+| **Sub-Agent Prompts** | 6 prompts — plan, review, tdd, security, architect, debugger |
 | **CLI Workflows** | 7 commands — tdd, review, plan, onboard, security-scan, refactor, handoff |
 | **Uninstall** | Full cleanup — 11 trace categories, interactive or auto |
 | **Metrics** | 7 metrics — TER, LR, CQI, BRR, TCGR, DCER, CTR |

package/adapters/claude-code/.claude/mcp.json

@@ -1,8 +1,8 @@
 {
   "mcpServers": {
     "milens": {
-      "command": "npx",
-      "args": ["milens", "serve"],
+      "command": "milens",
+      "args": ["serve", "-p", "."],
       "env": { "MILENS_PROFILE": "standard" }
     }
   }

package/adapters/claude-code/CLAUDE.md

@@ -45,7 +45,7 @@ All tool calls must include `repo` set to the absolute workspace root.
 
 ## Session Workflow
 
-1. **Start** — The milens MCP server connects via `npx milens serve`. Verify with `mcp_milens_status`.
+1. **Start** — The milens MCP server connects via `milens serve -p .`. Verify with `mcp_milens_status`.
 2. **Recall** — When asked to work on a symbol, use `mcp_milens_overview` for a combined view of context, impact, and text references.
 3. **Code** — Make changes following the edit-safety rules below.
 4. **Verify** — Before committing, run `mcp_milens_detect_changes` to confirm only expected files changed.

package/adapters/gemini/.gemini/context.md

@@ -22,8 +22,8 @@ This project is indexed by **milens**. You have MCP tools that are faster and mo
 {
   "mcpServers": {
     "milens": {
-      "command": "npx",
-      "args": ["milens", "serve"],
+      "command": "milens",
+      "args": ["serve", "-p", "${workspaceFolder}"],
       "env": { "MILENS_PROFILE": "standard" }
     }
   }

package/adapters/opencode/.opencode/config.json

@@ -1,9 +1,8 @@
 {
   "mcp": {
     "milens": {
-      "command": "npx",
-      "args": ["milens", "serve"],
-      "env": { "MILENS_PROFILE": "standard" }
+      "type": "local",
+      "command": ["milens", "serve", "-p", "."]
     }
   }
 }

package/adapters/zed/.zed/settings.json

@@ -1,7 +1,7 @@
 {
   "context_servers": {
     "milens": {
-      "command": "npx milens serve",
+      "command": "milens serve -p .",
       "env": { "MILENS_PROFILE": "minimal" }
     }
   }

package/dist/agents-md.d.ts

@@ -1,3 +1,4 @@
 import { Database } from './store/db.js';
+export declare function generateCrossRefSection(rootPath: string): string;
 export declare function generateAgentsMd(db: Database, rootPath: string): string;
 //# sourceMappingURL=agents-md.d.ts.map

package/dist/agents-md.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"agents-md.d.ts","sourceRoot":"","sources":["../src/agents-md.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,QAAQ,EAAE,MAAM,eAAe,CAAC;AA0CzC,wBAAgB,gBAAgB,CAAC,EAAE,EAAE,QAAQ,EAAE,QAAQ,EAAE,MAAM,GAAG,MAAM,CAiIvE"}
+{"version":3,"file":"agents-md.d.ts","sourceRoot":"","sources":["../src/agents-md.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,QAAQ,EAAE,MAAM,eAAe,CAAC;AAoDzC,wBAAgB,uBAAuB,CAAC,QAAQ,EAAE,MAAM,GAAG,MAAM,CAsChE;AAED,wBAAgB,gBAAgB,CAAC,EAAE,EAAE,QAAQ,EAAE,QAAQ,EAAE,MAAM,GAAG,MAAM,CAsIvE"}

package/dist/agents-md.js

@@ -1,4 +1,4 @@
-import { readFileSync } from 'node:fs';
+import { readFileSync, existsSync } from 'node:fs';
 import { join, relative, basename, dirname } from 'node:path';
 import { fileURLToPath } from 'node:url';
 const __dirname = dirname(fileURLToPath(import.meta.url));
@@ -35,6 +35,51 @@ function findRouteSymbols(db) {
     const routePatterns = /[\/\\]route\.[jt]sx?$|[\/\\]router[\/\\]|[\/\\]routes[\/\\]|[\/\\]api[\/\\]/;
     return all.filter(s => routePatterns.test(s.filePath) && s.exported && (s.kind === 'function' || s.kind === 'method' || s.kind === 'class'));
 }
+function loadCrossRefConfig(rootPath) {
+    const configPath = join(rootPath, '.milens-cross-ref.json');
+    try {
+        if (existsSync(configPath)) {
+            return JSON.parse(readFileSync(configPath, 'utf-8'));
+        }
+    }
+    catch { }
+    return null;
+}
+export function generateCrossRefSection(rootPath) {
+    const config = loadCrossRefConfig(rootPath);
+    if (!config || !config.repos || config.repos.length === 0)
+        return '';
+    const lines = [];
+    lines.push('<!-- AUTO-GENERATED by milens cross-ref hook — do not edit manually -->');
+    lines.push(`<!-- Last updated: ${new Date().toISOString()} -->`);
+    lines.push('');
+    lines.push('## Cross-Repository Context');
+    lines.push('');
+    lines.push('### Connected Repos');
+    lines.push('| Repo | Role | Visibility |');
+    lines.push('|------|------|------------|');
+    for (const repo of config.repos) {
+        const upstream = repo.isUpstream ? ' (upstream)' : '';
+        const license = repo.license ? ` ${repo.license}` : '';
+        lines.push(`| **${repo.name}**${upstream} | ${repo.role} | ${repo.visibility}${license} |`);
+    }
+    lines.push('');
+    if (config.contract) {
+        lines.push('### Contract');
+        lines.push(`- **Package:** ${config.contract.package} v${config.contract.version}`);
+        lines.push('');
+    }
+    if (config.dependencies && config.dependencies.length > 0) {
+        lines.push('### Key Dependencies');
+        lines.push('| Symbol | Source | Used By |');
+        lines.push('|--------|--------|---------|');
+        for (const d of config.dependencies) {
+            lines.push(`| \`${d.symbol}\` | ${d.source} | ${d.usedBy} |`);
+        }
+        lines.push('');
+    }
+    return lines.join('\n');
+}
 export function generateAgentsMd(db, rootPath) {
     const version = readMilensVersion();
     const date = new Date().toISOString().split('T')[0];
@@ -158,6 +203,10 @@ export function generateAgentsMd(db, rootPath) {
     lines.push('3. mcp_milens_annotate({symbol: "X", key: "note", value: "..."}) — save discoveries');
     lines.push('4. mcp_milens_session_end({session_id: "..."}) — record stats');
     lines.push('');
+    const crossRef = generateCrossRefSection(rootPath);
+    if (crossRef) {
+        lines.push(crossRef);
+    }
     return lines.join('\n');
 }
 //# sourceMappingURL=agents-md.js.map

package/dist/agents-md.js.map

@@ -1 +1 @@
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package/dist/analyzer/engine.d.ts

@@ -1,3 +1,4 @@
+import { type ProgressReporter } from '../ui/progress.js';
 import type { AnalysisStats } from '../types.js';
 import type Parser from 'web-tree-sitter';
 export declare function getCachedTree(filePath: string): Parser.Tree | undefined;
@@ -10,6 +11,7 @@ interface EngineOptions {
     aliases?: Record<string, string>;
     embeddings?: boolean;
     files?: string[];
+    onProgress?: ProgressReporter;
 }
 export declare function analyze(opts: EngineOptions): Promise<AnalysisStats>;
 export {};

package/dist/analyzer/engine.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"engine.d.ts","sourceRoot":"","sources":["../../src/analyzer/engine.ts"],"names":[],"mappings":"AAgBA,OAAO,KAAK,EAAyJ,aAAa,EAAE,MAAM,aAAa,CAAC;AACxM,OAAO,KAAK,MAAM,MAAM,iBAAiB,CAAC;AAO1C,wBAAgB,aAAa,CAAC,QAAQ,EAAE,MAAM,GAAG,MAAM,CAAC,IAAI,GAAG,SAAS,CAEvE;AACD,wBAAgB,cAAc,IAAI,IAAI,CAErC;AA8DD,UAAU,aAAa;IACrB,QAAQ,EAAE,MAAM,CAAC;IACjB,MAAM,EAAE,MAAM,CAAC;IACf,OAAO,CAAC,EAAE,OAAO,CAAC;IAClB,KAAK,CAAC,EAAE,OAAO,CAAC;IAChB,OAAO,CAAC,EAAE,MAAM,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC;IACjC,UAAU,CAAC,EAAE,OAAO,CAAC;IACrB,KAAK,CAAC,EAAE,MAAM,EAAE,CAAC;CAClB;AAqCD,wBAAsB,OAAO,CAAC,IAAI,EAAE,aAAa,GAAG,OAAO,CAAC,aAAa,CAAC,CAoWzE"}
+{"version":3,"file":"engine.d.ts","sourceRoot":"","sources":["../../src/analyzer/engine.ts"],"names":[],"mappings":"AAgBA,OAAO,EAAiB,KAAK,gBAAgB,EAAE,MAAM,mBAAmB,CAAC;AACzE,OAAO,KAAK,EAAyJ,aAAa,EAAE,MAAM,aAAa,CAAC;AACxM,OAAO,KAAK,MAAM,MAAM,iBAAiB,CAAC;AAO1C,wBAAgB,aAAa,CAAC,QAAQ,EAAE,MAAM,GAAG,MAAM,CAAC,IAAI,GAAG,SAAS,CAEvE;AACD,wBAAgB,cAAc,IAAI,IAAI,CAErC;AA8DD,UAAU,aAAa;IACrB,QAAQ,EAAE,MAAM,CAAC;IACjB,MAAM,EAAE,MAAM,CAAC;IACf,OAAO,CAAC,EAAE,OAAO,CAAC;IAClB,KAAK,CAAC,EAAE,OAAO,CAAC;IAChB,OAAO,CAAC,EAAE,MAAM,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC;IACjC,UAAU,CAAC,EAAE,OAAO,CAAC;IACrB,KAAK,CAAC,EAAE,MAAM,EAAE,CAAC;IACjB,UAAU,CAAC,EAAE,gBAAgB,CAAC;CAC/B;AAqCD,wBAAsB,OAAO,CAAC,IAAI,EAAE,aAAa,GAAG,OAAO,CAAC,aAAa,CAAC,CA8XzE"}

package/dist/analyzer/engine.js

@@ -14,6 +14,7 @@ import { enrichMetadata } from './enrich.js';
 import { isTestFile } from '../utils.js';
 import { Database } from '../store/db.js';
 import { TfIdfProvider, EmbeddingStore, buildEmbeddingText } from '../store/vectors.js';
+import { ProgressPhase } from '../ui/progress.js';
 // ── Cross-phase Tree Cache ──
 // Caches parsed syntax trees between parse and resolution phases
 // so scope-based resolvers can re-use trees without re-parsing.
@@ -108,20 +109,13 @@ export async function analyze(opts) {
     const rootPath = resolve(opts.rootPath);
     const db = new Database(opts.dbPath);
     const aliases = opts.aliases ?? {};
-    if (opts.force) {
-        if (opts.files && opts.files.length > 0) {
-            db.clearFiles(opts.files);
-        }
-        else {
-            db.clear();
-        }
-    }
+    const reporter = opts.onProgress;
     // Phase 1: Scan files (or use explicit file list for incremental)
     const files = opts.files && opts.files.length > 0
         ? scanFilesWithFilter(rootPath, opts.files, opts.verbose)
         : scanFiles(rootPath, opts.verbose);
     if (opts.verbose)
-        console.log(`[scan] Found ${files.length} source files`);
+        console.error(`[scan] Found ${files.length} source files`);
     // Phase 2: Group files by language for cache-friendly processing
     const langGroups = new Map();
     for (const file of files) {
@@ -152,6 +146,13 @@ export async function analyze(opts) {
     const parsedFiles = new Set();
     const importCache = new ImportResolveCache();
     let filesParsed = 0;
+    // Count total files for progress
+    let totalToParse = 0;
+    if (docGroup)
+        totalToParse += docGroup.length;
+    for (const [, group] of langGroups)
+        totalToParse += group.length;
+    reporter?.startPhase(ProgressPhase.PARSE, totalToParse);
     // Process document files (no tree-sitter needed) — batch read
     if (docGroup) {
         const docContents = await readFilesAsync(docGroup.map(f => f.absolutePath));
@@ -161,7 +162,7 @@ export async function analyze(opts) {
                 continue;
             if (!opts.force && db.isFileUpToDate(file.relativePath, source)) {
                 if (opts.verbose)
-                    console.log(`[skip] ${file.relativePath} (unchanged)`);
+                    console.error(`[skip] ${file.relativePath} (unchanged)`);
                 continue;
             }
             try {
@@ -180,8 +181,9 @@ export async function analyze(opts) {
                 db.upsertFileHash(file.relativePath, source);
                 parsedFiles.add(file.relativePath);
                 filesParsed++;
+                reporter?.tick(file.relativePath);
                 if (opts.verbose)
-                    console.log(`[parse] ${file.relativePath}: ${result.symbols.length} symbols`);
+                    console.error(`[parse] ${file.relativePath}: ${result.symbols.length} symbols`);
             }
             catch (err) {
                 if (opts.verbose)
@@ -215,7 +217,8 @@ export async function analyze(opts) {
                 // Skip unchanged files (incremental)
                 if (!opts.force && db.isFileUpToDate(file.relativePath, source)) {
                     if (opts.verbose)
-                        console.log(`[skip] ${file.relativePath} (unchanged)`);
+                        console.error(`[skip] ${file.relativePath} (unchanged)`);
+                    reporter?.tick();
                     continue;
                 }
                 try {
@@ -236,7 +239,7 @@ export async function analyze(opts) {
                     for (const imp of result.imports) {
                         const resolved = importCache.resolve(file.spec, imp.modulePath, imp.filePath, rootPath, aliases);
                         if (opts.verbose)
-                            console.log(`[resolve] ${imp.filePath}::${imp.modulePath} => ${resolved ?? 'NULL'}`);
+                            console.error(`[resolve] ${imp.filePath}::${imp.modulePath} => ${resolved ?? 'NULL'}`);
                         if (resolved) {
                             resolvedImportPaths.set(`${imp.filePath}::${imp.modulePath}`, resolved);
                         }
@@ -251,8 +254,9 @@ export async function analyze(opts) {
                     db.upsertFileHash(file.relativePath, source);
                     parsedFiles.add(file.relativePath);
                     filesParsed++;
+                    reporter?.tick(file.relativePath);
                     if (opts.verbose)
-                        console.log(`[parse] ${file.relativePath}: ${result.symbols.length} symbols`);
+                        console.error(`[parse] ${file.relativePath}: ${result.symbols.length} symbols`);
                 }
                 catch (err) {
                     if (opts.verbose)
@@ -262,6 +266,7 @@ export async function analyze(opts) {
             // chunkContents goes out of scope → GC can reclaim source strings
         }
     }
+    reporter?.endPhase();
     // Phase 4: Load unchanged files' symbols for cross-file resolution
     if (!opts.force) {
         for (const [, group] of langGroups) {
@@ -277,6 +282,7 @@ export async function analyze(opts) {
         }
     }
     // Phase 5: Resolve cross-file links
+    reporter?.startPhase(ProgressPhase.RESOLVE, 1);
     const perFileImportSemantics = new Map();
     const perFileMroStrategy = new Map();
     for (const [, group] of langGroups) {
@@ -306,16 +312,20 @@ export async function analyze(opts) {
     });
     const links = resolution.links;
     if (opts.verbose) {
-        console.log(`[link] Resolved ${links.length} relationships`);
+        console.error(`[link] Resolved ${links.length} relationships`);
         if (resolution.unresolvedImports > 0 || resolution.unresolvedCalls > 0) {
-            console.log(`[link] ⚠ ${resolution.unresolvedImports} unresolved imports, ${resolution.unresolvedCalls} unresolved calls (internal)`);
+            console.error(`[link] ⚠ ${resolution.unresolvedImports} unresolved imports, ${resolution.unresolvedCalls} unresolved calls (internal)`);
         }
         if (resolution.externalImports > 0 || resolution.externalCalls > 0) {
-            console.log(`[link] ✓ ${resolution.externalImports} external imports, ${resolution.externalCalls} external calls (expected)`);
+            console.error(`[link] ✓ ${resolution.externalImports} external imports, ${resolution.externalCalls} external calls (expected)`);
         }
     }
+    reporter?.endPhase();
     // Phase 5.5: Dual-path resolution — compare legacy vs scope-based
-    {
+    try {
+        const scopeT0 = Date.now();
+        if (opts.verbose)
+            console.error(`[dual] Starting scope-based resolution (${allSymbols.length} symbols, ${allCalls.length} calls, ${allImports.length} imports)...`);
         const scopeResolution = resolveWithScopes({
             symbolsByFile,
             allSymbols,
@@ -332,14 +342,20 @@ export async function analyze(opts) {
             perFileMroStrategy,
             treeCache,
         });
+        if (opts.verbose)
+            console.error(`[dual] Scope resolution completed in ${Date.now() - scopeT0}ms (${scopeResolution.links.length} links)`);
         const diffs = diffResolutions(resolution, scopeResolution);
         if (opts.verbose) {
             const matchPct = resolution.links.length > 0
                 ? ((resolution.links.length - diffs.length) / resolution.links.length * 100).toFixed(1)
                 : '0.0';
-            console.log(`[dual] Legacy: ${resolution.links.length} links, Scope: ${scopeResolution.links.length} links, Diff: ${diffs.length} (${matchPct}% match)`);
+            console.error(`[dual] Legacy: ${resolution.links.length} links, Scope: ${scopeResolution.links.length} links, Diff: ${diffs.length} (${matchPct}% match)`);
         }
     }
+    catch (err) {
+        if (opts.verbose)
+            console.error(`[dual] Scope resolution failed (non-fatal): ${err}`);
+    }
     // Release raw extraction data — no longer needed after resolution
     allImports.length = 0;
     allCalls.length = 0;
@@ -352,9 +368,11 @@ export async function analyze(opts) {
     resolvedImportPaths.clear();
     importCache.clear();
     // Phase 6: Enrich — compute roles, heat, zones from resolved graph
+    reporter?.startPhase(ProgressPhase.ENRICH, 1);
     const enriched = enrichMetadata({ symbols: allSymbols, links });
     if (opts.verbose)
-        console.log(`[enrich] Computed metadata for ${allSymbols.length} symbols, ${enriched.zones.size} zones`);
+        console.error(`[enrich] Computed metadata for ${allSymbols.length} symbols, ${enriched.zones.size} zones`);
+    reporter?.endPhase();
     // Phase 6.5: Test coverage — count symbols referenced from test files
     const testFileSymbolIds = new Set();
     const testFiles = new Set();
@@ -377,9 +395,15 @@ export async function analyze(opts) {
     }
     const exportedProduction = allSymbols.filter(s => s.exported && !isTestFile(s.filePath));
     // Phase 7: Persist to database in single transaction
+    reporter?.startPhase(ProgressPhase.PERSIST, 1);
     db.transaction(() => {
         if (opts.force) {
-            db.clearSymbolsAndLinks();
+            if (opts.files && opts.files.length > 0) {
+                db.clearFiles(opts.files);
+            }
+            else {
+                db.clear();
+            }
         }
         else {
             for (const fp of parsedFiles)
@@ -410,6 +434,7 @@ export async function analyze(opts) {
         db.setMeta('exported_production_symbols', String(exportedProduction.length));
         db.rebuildSearch();
     });
+    reporter?.endPhase();
     // Phase 8: Generate embeddings (optional)
     if (opts.embeddings) {
         const provider = new TfIdfProvider();
@@ -433,7 +458,7 @@ export async function analyze(opts) {
             embedded += batch.length;
         }
         if (opts.verbose)
-            console.log(`[embed] Generated ${embedded} embeddings (${provider.name})`);
+            console.error(`[embed] Generated ${embedded} embeddings (${provider.name})`);
     }
     const stats = {
         filesScanned: files.length,
@@ -447,11 +472,18 @@ export async function analyze(opts) {
         externalCalls: resolution.externalCalls,
     };
     if (opts.verbose) {
-        console.log(`[done] ${stats.symbolCount} symbols, ${stats.linkCount} links in ${stats.durationMs}ms`);
+        console.error(`[done] ${stats.symbolCount} symbols, ${stats.linkCount} links in ${stats.durationMs}ms`);
     }
+    reporter?.done(stats);
+    reporter?.finalize();
     clearQueryCache();
     clearTreeCache();
-    db.close();
+    try {
+        db.close();
+    }
+    finally {
+        // ensure close even on error
+    }
     return stats;
 }
 async function parseFile(source, filePath, spec, parser, lang) {