@monoes/monograph 1.6.0 → 1.6.2

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

@@ -1 +1 @@
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+{"version":3,"file":"orchestrator.d.ts","sourceRoot":"","sources":["../../../src/pipeline/orchestrator.ts"],"names":[],"mappings":"AAOA,OAAO,KAAK,EAAE,gBAAgB,EAAqB,MAAM,aAAa,CAAC;AAuBvE,OAAO,KAAK,EAAmB,eAAe,EAAE,MAAM,YAAY,CAAC;AAWnE,MAAM,WAAW,YAAa,SAAQ,OAAO,CAAC,eAAe,CAAC;IAC5D,UAAU,CAAC,EAAE,CAAC,CAAC,EAAE,gBAAgB,KAAK,IAAI,CAAC;IAC3C,KAAK,CAAC,EAAE,OAAO,CAAC;IAChB,oGAAoG;IACpG,WAAW,CAAC,EAAE,OAAO,CAAC;CACvB;AAkDD,wBAAsB,UAAU,CAAC,QAAQ,EAAE,MAAM,EAAE,OAAO,GAAE,YAAiB,GAAG,OAAO,CAAC,IAAI,CAAC,CAe5F;AAwPD;;;;;;;;;;;;;;;;GAgBG;AACH,wBAAsB,qBAAqB,CACzC,QAAQ,EAAE,MAAM,EAChB,eAAe,EAAE,MAAM,EAAE,EACzB,OAAO,GAAE,YAAiB,GACzB,OAAO,CAAC,IAAI,CAAC,CAUf"}

package/dist/src/pipeline/orchestrator.js

@@ -1,14 +1,11 @@
 import { execSync } from 'node:child_process';
-import { existsSync, readFileSync, statSync } from 'node:fs';
-import { extname, join, resolve } from 'node:path';
+import { join, resolve } from 'node:path';
 import Graph from 'graphology';
 import { analyzeChurn } from '../analysis/churn.js';
 import { ExtractionCache } from '../cache/extraction-cache.js';
-import { isSupportedExtension, parseFile } from '../parsers/loader.js';
 import { generateGraphReport } from '../reporting/graph-report.js';
 import { closeDb, openDb } from '../storage/db.js';
-import { deleteEdgesForFile, insertEdges } from '../storage/edge-store.js';
-import { deleteNodesForFile, insertNodes } from '../storage/node-store.js';
+import { isWithinScope, readIndexScope, scopeForOptions, writeIndexScope } from './index-scope.js';
 import { bridgeResolverPhase } from './phases/bridge-resolver.js';
 import { communitiesPhase } from './phases/communities.js';
 import { crossFilePhase } from './phases/cross-file.js';
@@ -18,7 +15,7 @@ import { importResolverPhase } from './phases/import-resolver.js';
 import { markdownPhase } from './phases/markdown.js';
 import { mroPhase } from './phases/mro.js';
 import { ormPhase } from './phases/orm.js';
-import { extractArrowFunctions, extractCsharpNamespaces, parsePhase } from './phases/parse.js';
+import { parsePhase } from './phases/parse.js';
 import { processesPhase } from './phases/processes.js';
 import { routesPhase } from './phases/routes.js';
 import { scanPhase } from './phases/scan.js';
@@ -27,7 +24,6 @@ import { structurePhase } from './phases/structure.js';
 import { suggestPhase } from './phases/suggest.js';
 import { surprisesPhase } from './phases/surprises.js';
 import { toolsPhase } from './phases/tools.js';
-import { extractVariables, variableToNode } from './phases/variables.js';
 import { variablesPhase } from './phases/variables-phase.js';
 import { wildcardSynthesisPhase } from './phases/wildcard-phase.js';
 import { PipelineRunner } from './runner.js';
@@ -121,7 +117,15 @@ async function buildAsyncLocked(repoPath, dbPath, fullOptions, options) {
             const tmpDb = openDb(dbPath);
             try {
                 const report = checkStaleness(tmpDb, resolve(repoPath));
-                if (!report.isStale && report.currentCommit !== null) {
+                // Gate on the explicit state, not the legacy `isStale` boolean.
+                // `isStale` only reflects commit divergence, so it stays false for an
+                // index whose commit matches HEAD but whose worktree has uncommitted
+                // edits — this guard would then skip the very rebuild those edits
+                // require. It is also false when git is unavailable, where nothing is
+                // actually known. `state === 'fresh'` is true only when the commit
+                // matches AND the worktree is clean AND that was determinable, so it
+                // subsumes the old currentCommit !== null check.
+                if (report.state === 'fresh') {
                     options.onProgress?.({ phase: 'skip', message: 'Index is fresh — skipping rebuild' });
                     return; // Already up-to-date
                 }
@@ -151,6 +155,16 @@ async function buildAsyncLocked(repoPath, dbPath, fullOptions, options) {
         }
     }
     const db = openDb(dbPath);
+    // Source-scope continuity (issue: a code-only auto-refresh wiped every
+    // previously-indexed Document node). A caller that doesn't state a scope
+    // inherits whatever the index was last built with, so a refresh can never
+    // silently narrow coverage; an explicit `codeOnly` from the caller still wins.
+    const storedScope = readIndexScope(db);
+    if (options.codeOnly === undefined && storedScope !== null) {
+        fullOptions.codeOnly = storedScope === 'code';
+    }
+    const activeScope = scopeForOptions(fullOptions.codeOnly);
+    options.onProgress?.({ phase: 'scope', message: `Index scope: ${activeScope}` });
     // The whole build is one SQL transaction: a phase throwing (e.g. issue
     // #40's FK violation) used to leave whatever earlier phases had already
     // autocommitted sitting in the DB, silently corrupting the index into a
@@ -216,12 +230,18 @@ async function buildAsyncLocked(repoPath, dbPath, fullOptions, options) {
         // (ctx.allFilesCached === true), a file may have been deleted from disk between
         // builds, which produces zero cache misses but still leaves ghost rows in the DB
         // unless we compare the DB's known file set against the current on-disk set.
+        //
+        // The sweep is confined to the current build's source domain (`activeScope`).
+        // A narrowed build never looked at files outside its domain, so their absence
+        // from `filePaths` says nothing about whether they still exist on disk —
+        // deleting those rows is how a code-only refresh used to erase every Document
+        // node in the graph.
         const scanOut = outputs.get('scan');
         if (scanOut) {
             const liveFiles = new Set(scanOut.filePaths.map((f) => resolve(f)));
             const staleFiles = db.prepare('SELECT DISTINCT file_path FROM nodes WHERE file_path IS NOT NULL').all()
                 .map((r) => r.file_path)
-                .filter((f) => !liveFiles.has(resolve(ctx.repoPath, f)));
+                .filter((f) => isWithinScope(f, activeScope) && !liveFiles.has(resolve(ctx.repoPath, f)));
             if (staleFiles.length > 0) {
                 const deleteStale = db.transaction((files) => {
                     const deleteEdges = db.prepare(`
@@ -278,6 +298,7 @@ async function buildAsyncLocked(repoPath, dbPath, fullOptions, options) {
             }
         }
         db.prepare("INSERT OR REPLACE INTO index_meta VALUES ('indexed_at', ?)").run(new Date().toISOString());
+        writeIndexScope(db, activeScope);
         db.exec('COMMIT');
         // Skip expensive report regeneration when all files were cached (nothing changed) —
         // this is purely a performance optimization, not correctness-critical, so it stays
@@ -312,121 +333,33 @@ async function buildAsyncLocked(repoPath, dbPath, fullOptions, options) {
         closeDb(db);
     }
 }
-const INCREMENTAL_THRESHOLD = 20;
+/**
+ * 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 async function buildIncrementalAsync(repoPath, changedAbsPaths, options = {}) {
     if (changedAbsPaths.length === 0)
         return;
-    if (changedAbsPaths.length > INCREMENTAL_THRESHOLD) {
-        return buildAsync(repoPath, options);
-    }
-    const dbPath = resolve(join(repoPath, '.monomind', 'monograph.db'));
-    if (!existsSync(dbPath)) {
-        return buildAsync(repoPath, options);
-    }
-    const releaseLock = await acquireBuildLock(dbPath);
-    if (!releaseLock) {
-        options.onProgress?.({
-            phase: 'skip',
-            message: 'Another build is in progress — skipping incremental',
-        });
-        return;
-    }
-    try {
-        await buildIncrementalLocked(resolve(repoPath), dbPath, changedAbsPaths, options);
-    }
-    finally {
-        releaseLock();
-    }
-}
-async function buildIncrementalLocked(resolvedRepo, dbPath, changedAbsPaths, options) {
-    const db = openDb(dbPath);
-    const maxSize = options.maxFileSizeBytes ?? DEFAULT_OPTIONS.maxFileSizeBytes;
-    db.exec('BEGIN');
-    try {
-        let parsed = 0;
-        let deleted = 0;
-        for (const absPath of changedAbsPaths) {
-            const ext = extname(absPath).toLowerCase();
-            if (!isSupportedExtension(ext))
-                continue;
-            if (ext === '.md' || ext === '.markdown')
-                continue;
-            const relPath = absPath.startsWith(resolvedRepo)
-                ? absPath.slice(resolvedRepo.length + 1)
-                : absPath;
-            deleteEdgesForFile(db, relPath);
-            deleteNodesForFile(db, relPath);
-            if (!existsSync(absPath)) {
-                deleted++;
-                continue;
-            }
-            let source;
-            try {
-                const stat = statSync(absPath);
-                if (stat.size > maxSize)
-                    continue;
-                source = readFileSync(absPath, 'utf-8');
-            }
-            catch {
-                continue;
-            }
-            const result = await parseFile(absPath, source, relPath);
-            const nodes = [...result.nodes];
-            const edges = [...result.edges];
-            if (ext === '.cs') {
-                for (const ns of extractCsharpNamespaces(source, relPath)) {
-                    nodes.push({
-                        id: `${ns.filePath}::namespace::${ns.name}`,
-                        name: ns.name,
-                        label: 'Namespace',
-                        normLabel: 'namespace',
-                        filePath: ns.filePath,
-                        line: ns.line,
-                        isExported: true,
-                    });
-                }
-            }
-            if (['.ts', '.tsx', '.js', '.jsx'].includes(ext)) {
-                const varInfos = extractVariables(source, relPath);
-                nodes.push(...varInfos.map((v) => variableToNode(v)));
-                for (const fn of extractArrowFunctions(source, relPath)) {
-                    nodes.push({
-                        id: `${fn.filePath}::fn::${fn.name}`,
-                        name: fn.name,
-                        label: 'Function',
-                        normLabel: 'function',
-                        filePath: fn.filePath,
-                        line: fn.line,
-                        isExported: fn.isExported,
-                    });
-                }
-            }
-            insertNodes(db, nodes);
-            insertEdges(db, edges);
-            parsed++;
-        }
-        const hash = getCurrentCommitHash(resolvedRepo);
-        if (hash) {
-            db.prepare("INSERT OR REPLACE INTO index_meta VALUES ('last_commit_hash', ?)").run(hash);
-        }
-        db.prepare("INSERT OR REPLACE INTO index_meta VALUES ('indexed_at', ?)").run(new Date().toISOString());
-        db.exec('COMMIT');
-        options.onProgress?.({
-            phase: 'incremental',
-            message: `Incremental: ${parsed} re-parsed, ${deleted} removed`,
-        });
-    }
-    catch (err) {
-        try {
-            db.exec('ROLLBACK');
-        }
-        catch {
-            /* ignore */
-        }
-        throw err;
-    }
-    finally {
-        closeDb(db);
-    }
+    // `incremental` means "skip when the index is already fresh", which is keyed on
+    // git HEAD. A working-tree edit doesn't move HEAD, so honouring the flag here
+    // would skip the very rebuild the caller just asked for.
+    await buildAsync(repoPath, { ...options, incremental: false });
+    options.onProgress?.({
+        phase: 'incremental',
+        message: `Rebuilt after ${changedAbsPaths.length} changed file(s)`,
+    });
 }
 //# sourceMappingURL=orchestrator.js.map

package/dist/src/pipeline/orchestrator.js.map

@@ -1 +1 @@
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package/dist/src/pipeline/phases/communities.d.ts

@@ -1,9 +1,60 @@
+import type { MonographDb } from '../../storage/db.js';
+import type { EdgeRelation } from '../../types.js';
 import type { PipelinePhase } from '../types.js';
 export interface CommunitiesOutput {
     memberships: Map<string, number>;
     communityLabels: Map<number, string>;
     cohesionScores: Map<number, number>;
 }
+/**
+ * The relation families that participate in clustering, and the weight each
+ * family contributes to the clustering graph.
+ *
+ * This selection is deliberate, not incidental: different relations mean very
+ * different things structurally, so they must not all count as the same
+ * evidence of coupling.
+ *
+ * - **Coupling (weight 1)** — one symbol genuinely depends on another at
+ *   runtime or type-check time. These are what a module boundary is supposed
+ *   to contain, so they drive cluster boundaries.
+ * - **Weak coupling (weight 0.5)** — real but indirect or partial links
+ *   (pass-through re-exports, member access, framework wiring). They pull
+ *   nodes together, but should not outvote a direct call or import.
+ * - **Containment (weight 0.25)** — a file *owns* a symbol; it is not evidence
+ *   that the two are coupled. Counted at full weight, containment dominates
+ *   every real repo (there is one CONTAINS edge per symbol) and clustering
+ *   degenerates into a restatement of the file tree. It is kept at a low weight
+ *   only so that symbols with no coupling edges still attach to their parent
+ *   rather than dropping out of the clustering entirely.
+ *
+ * Everything not listed is excluded: process/step relations (produced after
+ * this phase runs), and the document-knowledge-graph families (REFERENCES,
+ * PARENT_SECTION, TAGGED_AS, CO_OCCURS and the LLM-inferred prose relations),
+ * which describe prose adjacency rather than code coupling.
+ */
+export declare const CLUSTERING_RELATION_WEIGHTS: Readonly<Partial<Record<EdgeRelation, number>>>;
+export interface ClusteringEdge {
+    sourceId: string;
+    targetId: string;
+    weight: number;
+}
+/**
+ * Read the clustering input from the committed canonical graph — the `edges`
+ * table this build has already written — rather than from any single phase's
+ * in-memory output.
+ *
+ * This is the whole point of the query: edges produced by the resolution
+ * phases (scope-resolution's resolved CALLS, bridge-resolver, wildcard
+ * synthesis, mro, routes/tools/orm) are inserted straight into the DB and
+ * never surface in `parse` or `cross-file` phase output. Clustering from those
+ * outputs therefore ran over a thinner graph than the one every other consumer
+ * queries. Reading the table means clustering sees exactly the edges the rest
+ * of the system sees — filtered to the families selected above.
+ *
+ * The phase runs inside the build's open transaction on the same connection,
+ * so it observes this build's writes.
+ */
+export declare function loadClusteringEdges(db: MonographDb): ClusteringEdge[];
 export declare function computeCohesion(communityId: number, memberships: Map<string, number>, edges: Array<{
     sourceId: string;
     targetId: string;
@@ -14,14 +65,39 @@ export declare function computeCohesion(communityId: number, memberships: Map<st
  * This replaces calling `computeCohesion` inside a loop, which was O(K*(N+E))
  * because each call re-scanned all memberships (O(N)) and all edges (O(E)).
  *
+ * The score is a structural measurement — the fraction of possible internal
+ * pairs that are actually connected by a selected edge — and nothing more. It
+ * is not a quality, health, or design-correctness judgment: a low score says
+ * the clustering grouped nodes that have few links *among the relation
+ * families listed in CLUSTERING_RELATION_WEIGHTS*, which can equally mean the
+ * coupling is real but expressed through a family this phase excludes.
+ *
  * @param memberships - nodeId → communityId map from the clustering step
- * @param edges - all edges used for the graph (IMPORTS + resolved)
- * @returns Map of communityId → cohesion score ∈ [0, 1]
+ * @param edges - the same selected edge set that was clustered (see
+ *   `loadClusteringEdges`), so the score describes the graph that produced the
+ *   communities rather than some other edge set
+ * @returns Map of communityId → internal-edge density ∈ [0, 1]
  */
 export declare function computeAllCohesionScores(memberships: Map<string, number>, edges: Array<{
     sourceId: string;
     targetId: string;
 }>): Map<number, number>;
+/**
+ * Community detection over the committed canonical graph.
+ *
+ * What the output does and does not claim: communities here are the clusters
+ * a modularity-maximising algorithm (Leiden-style refinement over Louvain)
+ * finds in the weighted edge set defined by `CLUSTERING_RELATION_WEIGHTS`.
+ * They are a summary of *that* connectivity, and they have not been measured
+ * against package manifests, directory layout, or runtime deployment units —
+ * so a community is a candidate grouping to look at, not a verified
+ * architectural module or package boundary. Any consumer that presents these
+ * as architecture should say which basis it is using.
+ *
+ * `deps` lists every phase that writes a selected relation family into
+ * `edges`, so that the table is complete when this phase reads it. Adding a
+ * phase that emits a clustering relation means adding it here too.
+ */
 export declare const communitiesPhase: PipelinePhase<CommunitiesOutput>;
 /**
  * Split a community that is too large into smaller sub-groups.

package/dist/src/pipeline/phases/communities.d.ts.map

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