@monoes/monograph 1.6.1 → 1.6.3

package/dist/src/mcp-tools/query.js

@@ -1,10 +1,11 @@
 import { join } from 'node:path';
+import { searchGraph } from '../search/hybrid-query.js';
 import { closeDb, openDb } from '../storage/db.js';
-import { hybridSearch } from '../storage/fts-store.js';
 export const monographQueryTool = {
     name: 'monograph_query',
-    description: 'Keyword + fuzzy + LIKE hybrid search across the monograph knowledge graph. ' +
-        'Returns symbols and process nodes ranked by combined BM25 + subsequence + node-type bonus.',
+    description: 'Lexical keyword search across the monograph knowledge graph. ' +
+        'mode=hybrid (default) ranks by BM25 + LIKE fallback + subsequence fuzzy + node-type bonus; ' +
+        'mode=bm25 is BM25 only. Higher score = better match.',
     inputSchema: {
         type: 'object',
         properties: {
@@ -15,11 +16,16 @@ export const monographQueryTool = {
                 type: 'boolean',
                 description: 'Include Process nodes in results (default: true)',
             },
+            mode: {
+                type: 'string',
+                enum: ['bm25', 'hybrid'],
+                description: 'Retrieval mode (default: hybrid)',
+            },
         },
         required: ['query'],
     },
     async handler(args) {
-        const { query, repoPath, topK = 20, includeProcesses = true } = args;
+        const { query, repoPath, topK = 20, includeProcesses = true, mode = 'hybrid' } = args;
         let db = null;
         let shouldClose = false;
         if (args.db) {
@@ -33,10 +39,10 @@ export const monographQueryTool = {
             return { query, results: [], processCount: 0, symbolCount: 0 };
         }
         try {
-            // Route through hybridSearch (BM25 + LIKE + in-memory fuzzy + node-type bonus)
-            // — the same ranker the CLI uses. The previous hybridQuery call was BM25-only,
-            // so MCP users got weaker ranking than CLI users for the same graph.
-            const hits = hybridSearch(db, query, topK * 3);
+            // Route through the shared searchGraph service — the same retrieval the
+            // CLI-hosted monograph_query tool uses, so both adapters answer the same
+            // question the same way.
+            const hits = searchGraph(db, query, { limit: topK * 3, mode });
             const results = hits
                 .filter((h) => includeProcesses || h.label !== 'Process')
                 .map((h) => ({
@@ -45,7 +51,7 @@ export const monographQueryTool = {
                 name: h.name ?? h.id,
                 filePath: h.filePath ?? undefined,
                 startLine: h.startLine ?? null,
-                score: h.combinedScore,
+                score: h.relevance,
                 isProcess: h.label === 'Process',
             }))
                 .slice(0, topK);

package/dist/src/mcp-tools/query.js.map

@@ -1 +1 @@
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package/dist/src/mcp-tools/rename.d.ts.map

@@ -1 +1 @@
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package/dist/src/mcp-tools/rename.js

@@ -1,5 +1,24 @@
 import { readFileSync, statSync } from 'node:fs';
+import { dirname, resolve } from 'node:path';
 import { rowToNode } from '../storage/node-store.js';
+// ── Repo root resolution ───────────────────────────────────────────────────────
+/**
+ * Node rows store repo-relative paths, but this function is handed only the DB
+ * connection (the MCP adapter opens the DB and passes nothing else). The index
+ * always lives at `<repoRoot>/.monomind/monograph.db` — see
+ * `pipeline/orchestrator.ts` and `mcp/resources.ts`, which both derive the DB
+ * path that way — so the repo root is the DB file's grandparent directory.
+ *
+ * Without this, every filesystem read here resolved against `process.cwd()`,
+ * which is only the indexed repo by accident: the MCP server locates the DB via
+ * MONOMIND_CWD / the git root, not via cwd, so renames reported zero changes.
+ */
+function repoRootFromDb(db) {
+    const dbPath = db.name;
+    if (!dbPath || dbPath === ':memory:')
+        return null;
+    return dirname(dirname(resolve(dbPath)));
+}
 // ── Implementation ─────────────────────────────────────────────────────────────
 export function getMonographRename(db, input) {
     // Find the canonical node
@@ -33,16 +52,22 @@ export function getMonographRename(db, input) {
     const MAX_FILE_BYTES = 1_048_576; // 1 MiB guard
     // File line cache to avoid re-reading the same file multiple times
     const fileLineCache = new Map();
+    const repoRoot = repoRootFromDb(db);
     const getLines = (filePath) => {
         if (fileLineCache.has(filePath))
             return fileLineCache.get(filePath);
+        // Rows hold repo-relative paths; an absolute one resolves to itself.
+        const absPath = resolve(repoRoot ?? '.', filePath);
         try {
-            const st = statSync(filePath);
+            // A file recorded in the graph may have been deleted or moved since the
+            // last build — statSync/readFileSync throw, and the catch below records an
+            // empty file so the rename simply reports no changes for it.
+            const st = statSync(absPath);
             if (st.size > MAX_FILE_BYTES) {
                 fileLineCache.set(filePath, []);
                 return [];
             }
-            const content = readFileSync(filePath, 'utf-8');
+            const content = readFileSync(absPath, 'utf-8');
             const lines = content.split('\n');
             fileLineCache.set(filePath, lines);
             return lines;

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package/dist/src/parsers/extractor.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"extractor.d.ts","sourceRoot":"","sources":["../../../src/parsers/extractor.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,MAAM,iBAAiB,CAAC;AAG1C,OAAO,KAAK,EAAE,cAAc,EAAE,MAAM,sBAAsB,CAAC;AAC3D,OAAO,KAAK,EAAE,WAAW,EAAE,MAAM,aAAa,CAAC;AAE/C,wBAAgB,cAAc,CAC5B,IAAI,EAAE,MAAM,CAAC,IAAI,EACjB,MAAM,EAAE,MAAM,EACd,QAAQ,EAAE,MAAM,EAChB,MAAM,EAAE,cAAc,EACtB,GAAG,EAAE,MAAM,GACV,WAAW,CA2Ib"}
+{"version":3,"file":"extractor.d.ts","sourceRoot":"","sources":["../../../src/parsers/extractor.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,MAAM,iBAAiB,CAAC;AAG1C,OAAO,KAAK,EAAE,cAAc,EAAE,MAAM,sBAAsB,CAAC;AAC3D,OAAO,KAAK,EAAE,WAAW,EAAE,MAAM,aAAa,CAAC;AAE/C,wBAAgB,cAAc,CAC5B,IAAI,EAAE,MAAM,CAAC,IAAI,EACjB,MAAM,EAAE,MAAM,EACd,QAAQ,EAAE,MAAM,EAChB,MAAM,EAAE,cAAc,EACtB,GAAG,EAAE,MAAM,GACV,WAAW,CAoJb"}

package/dist/src/parsers/extractor.js

@@ -1,13 +1,20 @@
-import { CONFIDENCE_SCORE, makeId, toNormLabel } from '../types.js';
+import { CONFIDENCE_SCORE, fileId, makeId, symbolId, toNormLabel } from '../types.js';
 export function extractSymbols(tree, source, repoPath, config, ext) {
     const nodes = [];
     const edges = [];
     const parseErrors = [];
     const language = config.name;
-    function nodeId(name, filePath, extra) {
-        return makeId(filePath.replace(/\//g, '_'), name, extra ?? '');
+    // Same (scope, name, kind) can legitimately recur in one file — C++/Java
+    // overloads, conditionally compiled or repeated definitions. Count occurrences
+    // in walk order (deterministic) so each gets a distinct overload discriminator.
+    const overloadCounts = new Map();
+    function symbolNodeId(scope, name, kind) {
+        const first = symbolId({ filePath: repoPath, scope, name, kind });
+        const overload = overloadCounts.get(first) ?? 0;
+        overloadCounts.set(first, overload + 1);
+        return overload === 0 ? first : symbolId({ filePath: repoPath, scope, name, kind, overload });
     }
-    const fileNodeId = makeId(repoPath.replace(/\//g, '_'), 'file');
+    const fileNodeId = fileId(repoPath);
     nodes.push({
         id: fileNodeId,
         label: 'File',
@@ -17,7 +24,7 @@ export function extractSymbols(tree, source, repoPath, config, ext) {
         isExported: false,
         language,
     });
-    function walk(node, parentId) {
+    function walk(node, parentId, scope = []) {
         // Skip anonymous keyword tokens — some grammars type them identically to
         // declaration nodes (tree-sitter-ruby's class keyword is a node of type
         // 'class'), which would otherwise produce spurious symbols named after the
@@ -61,7 +68,7 @@ export function extractSymbols(tree, source, repoPath, config, ext) {
                                     ? 'Constructor'
                                     : 'Function';
             const label = config.labelRefiner ? config.labelRefiner(node, rawLabel) : rawLabel;
-            const id = nodeId(name, repoPath, label.toLowerCase());
+            const id = symbolNodeId(scope, name, label);
             const isExported = config.exportDetector
                 ? config.exportDetector(node, source)
                 : isNodeExported(node, source);
@@ -86,13 +93,14 @@ export function extractSymbols(tree, source, repoPath, config, ext) {
                 confidenceScore: CONFIDENCE_SCORE.EXTRACTED,
             });
             handleInheritance(node, id, edges, repoPath, config, source);
+            const childScope = [...scope, name];
             for (let i = 0; i < node.childCount; i++) {
-                walk(node.child(i), id);
+                walk(node.child(i), id, childScope);
             }
             return;
         }
         for (let i = 0; i < node.childCount; i++) {
-            walk(node.child(i), parentId);
+            walk(node.child(i), parentId, scope);
         }
     }
     walk(tree.rootNode);

package/dist/src/parsers/extractor.js.map

@@ -1 +1 @@
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+{"version":3,"file":"extractor.js","sourceRoot":"","sources":["../../../src/parsers/extractor.ts"],"names":[],"mappings":"AAEA,OAAO,EAAE,gBAAgB,EAAE,MAAM,EAAE,MAAM,EAAE,QAAQ,EAAE,WAAW,EAAE,MAAM,aAAa,CAAC;AAItF,MAAM,UAAU,cAAc,CAC5B,IAAiB,EACjB,MAAc,EACd,QAAgB,EAChB,MAAsB,EACtB,GAAW;IAEX,MAAM,KAAK,GAAoB,EAAE,CAAC;IAClC,MAAM,KAAK,GAAoB,EAAE,CAAC;IAClC,MAAM,WAAW,GAAa,EAAE,CAAC;IACjC,MAAM,QAAQ,GAAG,MAAM,CAAC,IAAI,CAAC;IAE7B,yEAAyE;IACzE,+EAA+E;IAC/E,gFAAgF;IAChF,MAAM,cAAc,GAAG,IAAI,GAAG,EAAkB,CAAC;IAEjD,SAAS,YAAY,CAAC,KAAwB,EAAE,IAAY,EAAE,IAAY;QACxE,MAAM,KAAK,GAAG,QAAQ,CAAC,EAAE,QAAQ,EAAE,QAAQ,EAAE,KAAK,EAAE,IAAI,EAAE,IAAI,EAAE,CAAC,CAAC;QAClE,MAAM,QAAQ,GAAG,cAAc,CAAC,GAAG,CAAC,KAAK,CAAC,IAAI,CAAC,CAAC;QAChD,cAAc,CAAC,GAAG,CAAC,KAAK,EAAE,QAAQ,GAAG,CAAC,CAAC,CAAC;QACxC,OAAO,QAAQ,KAAK,CAAC,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,QAAQ,CAAC,EAAE,QAAQ,EAAE,QAAQ,EAAE,KAAK,EAAE,IAAI,EAAE,IAAI,EAAE,QAAQ,EAAE,CAAC,CAAC;IAChG,CAAC;IAED,MAAM,UAAU,GAAG,MAAM,CAAC,QAAQ,CAAC,CAAC;IACpC,KAAK,CAAC,IAAI,CAAC;QACT,EAAE,EAAE,UAAU;QACd,KAAK,EAAE,MAAM;QACb,IAAI,EAAE,QAAQ,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC,GAAG,EAAE,IAAI,QAAQ;QAC3C,SAAS,EAAE,WAAW,CAAC,QAAQ,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC,GAAG,EAAE,IAAI,QAAQ,CAAC;QAC7D,QAAQ,EAAE,QAAQ;QAClB,UAAU,EAAE,KAAK;QACjB,QAAQ;KACT,CAAC,CAAC;IAEH,SAAS,IAAI,CAAC,IAAiB,EAAE,QAAiB,EAAE,KAAK,GAAsB,EAAE;QAC/E,yEAAyE;QACzE,wEAAwE;QACxE,2EAA2E;QAC3E,WAAW;QACX,IAAI,CAAC,IAAI,CAAC,OAAO;YAAE,OAAO;QAE1B,MAAM,EAAE,IAAI,EAAE,GAAG,IAAI,CAAC;QAEtB,IAAI,MAAM,CAAC,eAAe,CAAC,GAAG,CAAC,IAAI,CAAC,EAAE,CAAC;YACrC,YAAY,CAAC,IAAI,EAAE,UAAU,EAAE,MAAM,EAAE,MAAM,EAAE,KAAK,EAAE,QAAQ,CAAC,CAAC;YAChE,OAAO;QACT,CAAC;QAED,MAAM,OAAO,GAAG,MAAM,CAAC,cAAc,CAAC,GAAG,CAAC,IAAI,CAAC,CAAC;QAChD,MAAM,QAAQ,GAAG,MAAM,CAAC,eAAe,CAAC,GAAG,CAAC,IAAI,CAAC,CAAC;QAClD,MAAM,MAAM,GAAG,MAAM,CAAC,aAAa,CAAC,GAAG,CAAC,IAAI,CAAC,CAAC;QAC9C,MAAM,UAAU,GAAG,MAAM,CAAC,iBAAiB,CAAC,GAAG,CAAC,IAAI,CAAC,CAAC;QACtD,MAAM,QAAQ,GAAG,MAAM,CAAC,eAAe,CAAC,GAAG,CAAC,IAAI,CAAC,CAAC;QAClD,MAAM,WAAW,GAAG,MAAM,CAAC,kBAAkB,CAAC,GAAG,CAAC,IAAI,CAAC,CAAC;QACxD,MAAM,aAAa,GAAG,MAAM,CAAC,oBAAoB,CAAC,GAAG,CAAC,IAAI,CAAC,CAAC;QAE5D,IAAI,OAAO,IAAI,QAAQ,IAAI,MAAM,IAAI,UAAU,IAAI,QAAQ,IAAI,WAAW,IAAI,aAAa,EAAE,CAAC;YAC5F,MAAM,QAAQ,GAAG,IAAI,CAAC,iBAAiB,CAAC,MAAM,CAAC,SAAS,CAAC,CAAC;YAC1D,MAAM,OAAO,GAAG,QAAQ,EAAE,IAAI,IAAI,IAAI,CAAC,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC;YACxE,MAAM,IAAI,GAAG,MAAM,CAAC,WAAW,CAAC,CAAC,CAAC,MAAM,CAAC,WAAW,CAAC,IAAI,EAAE,OAAO,CAAC,CAAC,CAAC,CAAC,OAAO,CAAC;YAC9E,iFAAiF;YACjF,oFAAoF;YACpF,kFAAkF;YAClF,MAAM,uBAAuB,GAAG,UAAU,IAAI,QAAQ,CAAC;YACvD,MAAM,gBAAgB,GAAG,uBAAuB;gBAC9C,CAAC,CAAC,MAAM,CAAC,cAAc,CAAC,GAAG,CAAC,IAAI,CAAC,MAAM,EAAE,MAAM,EAAE,IAAI,IAAI,EAAE,CAAC;gBAC5D,CAAC,CAAC,QAAQ,CAAC;YACb,MAAM,QAAQ,GAAG,OAAO;gBACtB,CAAC,CAAC,OAAO;gBACT,CAAC,CAAC,QAAQ;oBACR,CAAC,CAAC,QAAQ;oBACV,CAAC,CAAC,MAAM;wBACN,CAAC,CAAC,MAAM;wBACR,CAAC,CAAC,WAAW;4BACX,CAAC,CAAC,WAAW;4BACb,CAAC,CAAC,gBAAgB;gCAChB,CAAC,CAAC,QAAQ;gCACV,CAAC,CAAC,aAAa;oCACb,CAAC,CAAC,aAAa;oCACf,CAAC,CAAC,UAAU,CAAC;YACzB,MAAM,KAAK,GAAG,MAAM,CAAC,YAAY,CAAC,CAAC,CAAC,MAAM,CAAC,YAAY,CAAC,IAAI,EAAE,QAAQ,CAAC,CAAC,CAAC,CAAC,QAAQ,CAAC;YACnF,MAAM,EAAE,GAAG,YAAY,CAAC,KAAK,EAAE,IAAI,EAAE,KAAK,CAAC,CAAC;YAC5C,MAAM,UAAU,GAAG,MAAM,CAAC,cAAc;gBACtC,CAAC,CAAC,MAAM,CAAC,cAAc,CAAC,IAAI,EAAE,MAAM,CAAC;gBACrC,CAAC,CAAC,cAAc,CAAC,IAAI,EAAE,MAAM,CAAC,CAAC;YAEjC,KAAK,CAAC,IAAI,CAAC;gBACT,EAAE;gBACF,KAAK;gBACL,IAAI;gBACJ,SAAS,EAAE,WAAW,CAAC,IAAI,CAAC;gBAC5B,QAAQ,EAAE,QAAQ;gBAClB,SAAS,EAAE,IAAI,CAAC,aAAa,CAAC,GAAG,GAAG,CAAC;gBACrC,OAAO,EAAE,IAAI,CAAC,WAAW,CAAC,GAAG,GAAG,CAAC;gBACjC,UAAU;gBACV,QAAQ;aACT,CAAC,CAAC;YAEH,MAAM,WAAW,GAAG,QAAQ,IAAI,UAAU,CAAC;YAC3C,KAAK,CAAC,IAAI,CAAC;gBACT,EAAE,EAAE,MAAM,CAAC,WAAW,EAAE,EAAE,EAAE,UAAU,CAAC;gBACvC,QAAQ,EAAE,WAAW;gBACrB,QAAQ,EAAE,EAAE;gBACZ,QAAQ,EAAE,UAAU;gBACpB,UAAU,EAAE,WAAW;gBACvB,eAAe,EAAE,gBAAgB,CAAC,SAAS;aAC5C,CAAC,CAAC;YAEH,iBAAiB,CAAC,IAAI,EAAE,EAAE,EAAE,KAAK,EAAE,QAAQ,EAAE,MAAM,EAAE,MAAM,CAAC,CAAC;YAE7D,MAAM,UAAU,GAAG,CAAC,GAAG,KAAK,EAAE,IAAI,CAAC,CAAC;YACpC,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,IAAI,CAAC,UAAU,EAAE,CAAC,EAAE,EAAE,CAAC;gBACzC,IAAI,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,CAAE,EAAE,EAAE,EAAE,UAAU,CAAC,CAAC;YACvC,CAAC;YACD,OAAO;QACT,CAAC;QAED,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,IAAI,CAAC,UAAU,EAAE,CAAC,EAAE,EAAE,CAAC;YACzC,IAAI,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,CAAE,EAAE,QAAQ,EAAE,KAAK,CAAC,CAAC;QACxC,CAAC;IACH,CAAC;IAED,IAAI,CAAC,IAAI,CAAC,QAAQ,CAAC,CAAC;IAEpB,wEAAwE;IACxE,0EAA0E;IAC1E,mDAAmD;IACnD,IACE,GAAG,KAAK,KAAK;QACb,GAAG,KAAK,MAAM;QACd,GAAG,KAAK,KAAK;QACb,GAAG,KAAK,MAAM;QACd,GAAG,KAAK,MAAM;QACd,GAAG,KAAK,MAAM,EACd,CAAC;QACD,MAAM,eAAe,GAAG,sDAAsD,CAAC;QAC/E,IAAI,OAA+B,CAAC;QACpC,OAAO,CAAC,OAAO,GAAG,eAAe,CAAC,IAAI,CAAC,MAAM,CAAC,CAAC,KAAK,IAAI,EAAE,CAAC;YACzD,MAAM,UAAU,GAAG,OAAO,CAAC,CAAC,CAAC,CAAC;YAC9B,mFAAmF;YACnF,MAAM,QAAQ,GAAG,MAAM,CAAC,QAAQ,EAAE,UAAU,CAAC,CAAC;YAC9C,KAAK,CAAC,IAAI,CAAC;gBACT,EAAE,EAAE,MAAM,CAAC,UAAU,EAAE,QAAQ,EAAE,WAAW,CAAC;gBAC7C,QAAQ,EAAE,UAAU;gBACpB,QAAQ;gBACR,QAAQ,EAAE,YAAY;gBACtB,UAAU,EAAE,WAAW;gBACvB,eA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package/dist/src/parsers/loader.js

@@ -2,7 +2,7 @@ import { readFile } from 'node:fs/promises';
 import { join } from 'node:path';
 import { fileURLToPath } from 'node:url';
 import { Language, Parser } from 'web-tree-sitter';
-import { CONFIDENCE_SCORE, makeId, toNormLabel } from '../types.js';
+import { CONFIDENCE_SCORE, fileId, makeId, symbolId, toNormLabel } from '../types.js';
 import { extractSymbolsForLanguage, LANGUAGE_EXTENSIONS } from './language-parsers.js';
 const parserCache = new Map();
 const configCache = new Map();
@@ -310,7 +310,7 @@ export async function parseFile(absolutePath, sourceText, repoRelativePath) {
 function convertSymbolExtracts(extracts, repoRelativePath, language) {
     const nodes = [];
     const edges = [];
-    const fileNodeId = makeId(repoRelativePath.replace(/\//g, '_'), 'file');
+    const fileNodeId = fileId(repoRelativePath);
     const fileName = repoRelativePath.split('/').pop() ?? repoRelativePath;
     nodes.push({
         id: fileNodeId,
@@ -321,9 +321,23 @@ function convertSymbolExtracts(extracts, repoRelativePath, language) {
         isExported: false,
         language,
     });
+    // Regex extraction is flat — it recovers no enclosing scope — so the overload
+    // discriminator is what separates repeated `name`/`label` pairs in one file.
+    const overloadCounts = new Map();
     for (const ex of extracts) {
         const label = ex.label;
-        const id = makeId(repoRelativePath.replace(/\//g, '_'), ex.name, label.toLowerCase());
+        const first = symbolId({ filePath: repoRelativePath, scope: [], name: ex.name, kind: label });
+        const overload = overloadCounts.get(first) ?? 0;
+        overloadCounts.set(first, overload + 1);
+        const id = overload === 0
+            ? first
+            : symbolId({
+                filePath: repoRelativePath,
+                scope: [],
+                name: ex.name,
+                kind: label,
+                overload,
+            });
         nodes.push({
             id,
             label,

package/dist/src/parsers/loader.js.map

@@ -1 +1 @@
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package/dist/src/pipeline/index-scope.d.ts

@@ -0,0 +1,23 @@
+import type { MonographDb } from '../storage/db.js';
+/**
+ * The source-selection domain a graph was built with. `code` is what a
+ * `codeOnly: true` scan looks at (files with a parseable code extension);
+ * `all` additionally covers documents, markdown, config and other text files.
+ *
+ * The scope is persisted with the index so a later refresh reuses it instead of
+ * silently narrowing coverage, and so the orphan sweep can tell "this file was
+ * deleted" apart from "this file was never in the scan's domain".
+ */
+export type IndexScope = 'code' | 'all';
+export declare function scopeForOptions(codeOnly: boolean): IndexScope;
+/** The scope the stored graph was last built with, or null if never recorded. */
+export declare function readIndexScope(db: MonographDb): IndexScope | null;
+export declare function writeIndexScope(db: MonographDb, scope: IndexScope): void;
+/**
+ * Whether `filePath` belongs to the source domain a build at `scope` actually
+ * scans. Rows outside the current scope's domain were produced by a wider
+ * earlier build and must be left alone — a code-only refresh never looked at
+ * those files, so their absence from its file list is not evidence of deletion.
+ */
+export declare function isWithinScope(filePath: string, scope: IndexScope): boolean;
+//# sourceMappingURL=index-scope.d.ts.map

package/dist/src/pipeline/index-scope.d.ts.map

@@ -0,0 +1 @@
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package/dist/src/pipeline/index-scope.js

@@ -0,0 +1,33 @@
+import { extname } from 'node:path';
+import { isSupportedExtension } from '../parsers/loader.js';
+const INDEX_SCOPE_KEY = 'source_scope';
+export function scopeForOptions(codeOnly) {
+    return codeOnly ? 'code' : 'all';
+}
+/** The scope the stored graph was last built with, or null if never recorded. */
+export function readIndexScope(db) {
+    try {
+        const row = db.prepare('SELECT value FROM index_meta WHERE key = ?').get(INDEX_SCOPE_KEY);
+        if (row?.value === 'code' || row?.value === 'all')
+            return row.value;
+        return null;
+    }
+    catch {
+        return null;
+    }
+}
+export function writeIndexScope(db, scope) {
+    db.prepare('INSERT OR REPLACE INTO index_meta VALUES (?, ?)').run(INDEX_SCOPE_KEY, scope);
+}
+/**
+ * Whether `filePath` belongs to the source domain a build at `scope` actually
+ * scans. Rows outside the current scope's domain were produced by a wider
+ * earlier build and must be left alone — a code-only refresh never looked at
+ * those files, so their absence from its file list is not evidence of deletion.
+ */
+export function isWithinScope(filePath, scope) {
+    if (scope === 'all')
+        return true;
+    return isSupportedExtension(extname(filePath).toLowerCase());
+}
+//# sourceMappingURL=index-scope.js.map

package/dist/src/pipeline/index-scope.js.map

@@ -0,0 +1 @@
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package/dist/src/pipeline/orchestrator.d.ts

@@ -7,5 +7,22 @@ export interface BuildOptions extends Partial<PipelineOptions> {
     incremental?: boolean;
 }
 export declare function buildAsync(repoPath: string, options?: BuildOptions): Promise<void>;
+/**
+ * Re-index after files changed on disk.
+ *
+ * This runs the FULL pipeline, with extraction-cache reuse so unchanged files
+ * are not re-parsed. The previous partial implementation deleted the changed
+ * files' edges, re-parsed only those files, and stopped — it never reran
+ * relationship resolution (imports, cross-file calls, scope/bridge resolution)
+ * or the derived analyses (communities, processes, god-nodes). A one-line edit
+ * therefore dropped every CALLS/IMPORTS/REFERENCES edge incident to that file
+ * and left derived analysis stale. The watcher's deferred full rebuild repaired
+ * that eventually; direct callers silently kept the incomplete graph.
+ *
+ * A genuine incremental path is still worth having, but it has to track the
+ * changed files' dependents, recompute their relationships, and invalidate the
+ * affected derived analyses. Until such an implementation exists and is proven
+ * equivalent to a clean build, correctness wins over speed.
+ */
 export declare function buildIncrementalAsync(repoPath: string, changedAbsPaths: string[], options?: BuildOptions): Promise<void>;
 //# sourceMappingURL=orchestrator.d.ts.map

package/dist/src/pipeline/orchestrator.d.ts.map

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