@monoes/monograph 1.6.0 → 1.6.2

package/dist/src/pipeline/phases/communities.js

@@ -1,6 +1,104 @@
+import Graph from 'graphology';
 import louvain from 'graphology-communities-louvain';
-import { loadGraphFromEdges } from '../../graph/loader.js';
 import { leiden } from './leiden.js';
+/**
+ * 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 const CLUSTERING_RELATION_WEIGHTS = {
+    // Coupling
+    CALLS: 1,
+    IMPORTS: 1,
+    EXTENDS: 1,
+    IMPLEMENTS: 1,
+    // Weak coupling
+    RE_EXPORTS: 0.5,
+    METHOD_OVERRIDES: 0.5,
+    METHOD_IMPLEMENTS: 0.5,
+    ACCESSES: 0.5,
+    QUERIES: 0.5,
+    FETCHES: 0.5,
+    HANDLES_ROUTE: 0.5,
+    HANDLES_TOOL: 0.5,
+    WRAPS: 0.5,
+    // Containment
+    CONTAINS: 0.25,
+    DEFINES: 0.25,
+    HAS_METHOD: 0.25,
+    HAS_PROPERTY: 0.25,
+    HAS_FIELD: 0.25,
+    MEMBER_OF: 0.25,
+};
+/**
+ * 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 function loadClusteringEdges(db) {
+    const relations = Object.keys(CLUSTERING_RELATION_WEIGHTS);
+    const placeholders = relations.map(() => '?').join(',');
+    const rows = db
+        .prepare(`SELECT source_id, target_id, relation FROM edges WHERE relation IN (${placeholders})`)
+        .all(...relations);
+    return rows.map((r) => ({
+        sourceId: r.source_id,
+        targetId: r.target_id,
+        weight: CLUSTERING_RELATION_WEIGHTS[r.relation] ?? 0,
+    }));
+}
+/**
+ * Build the weighted clustering graph. Louvain reads the `weight` attribute.
+ *
+ * The projection is **undirected**: "do these two symbols belong in the same
+ * group" is a symmetric question, and modularity is defined over undirected
+ * connectivity. Clustering the directed graph made the family weights above
+ * inert — directed modularity would split a caller from its callee even when
+ * the call edge was the heaviest link between them. A multigraph is used so
+ * that parallel links between the same pair (e.g. a call in both directions,
+ * or a call plus an import) add up rather than being discarded.
+ */
+function buildClusteringGraph(edges) {
+    const graph = new Graph({ multi: true, type: 'undirected' });
+    for (const edge of edges) {
+        graph.mergeNode(edge.sourceId);
+        graph.mergeNode(edge.targetId);
+        graph.addEdge(edge.sourceId, edge.targetId, { weight: edge.weight });
+    }
+    return graph;
+}
 export function computeCohesion(communityId, memberships, edges) {
     const members = [...memberships.entries()].filter(([, c]) => c === communityId).map(([id]) => id);
     const n = members.length;
@@ -30,9 +128,18 @@ export function computeCohesion(communityId, memberships, edges) {
  * 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 function computeAllCohesionScores(memberships, edges) {
     // Single pass over memberships: build communityId → Set<nodeId>
@@ -78,17 +185,42 @@ export function computeAllCohesionScores(memberships, edges) {
     }
     return scores;
 }
+/**
+ * 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 const communitiesPhase = {
     name: 'communities',
-    deps: ['parse', 'cross-file', 'mro'],
-    async execute(ctx, deps) {
+    deps: [
+        'parse',
+        'cross-file',
+        'mro',
+        'routes',
+        'tools',
+        'orm',
+        'import-resolver',
+        'scope-resolution',
+        'bridge-resolver',
+        'wildcard-synthesis',
+    ],
+    async execute(ctx) {
         if (ctx.allFilesCached) {
             return { memberships: new Map(), communityLabels: new Map(), cohesionScores: new Map() };
         }
-        const { resolvedEdges } = deps.get('cross-file');
-        const { allEdges } = deps.get('parse');
-        const allUsedEdges = [...allEdges, ...resolvedEdges];
-        const graph = loadGraphFromEdges(allUsedEdges);
+        const allUsedEdges = loadClusteringEdges(ctx.db);
+        const graph = buildClusteringGraph(allUsedEdges);
         let communities = {};
         try {
             communities = leiden(graph, { seed: 42 });

package/dist/src/pipeline/phases/communities.js.map

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package/dist/src/pipeline/phases/markdown.js

@@ -2,7 +2,7 @@ import { readFileSync, statSync } from 'node:fs';
 import { basename, extname } from 'node:path';
 import { insertEdges } from '../../storage/edge-store.js';
 import { insertNodes } from '../../storage/node-store.js';
-import { makeId, toNormLabel } from '../../types.js';
+import { docId, makeId, toNormLabel } from '../../types.js';
 const MARKDOWN_EXTENSIONS = new Set(['.md', '.mdx']);
 // Inline code span: `identifier`
 const INLINE_CODE_RE = /`([^`]+)`/g;
@@ -39,10 +39,10 @@ export const markdownPhase = {
                 continue;
             }
             const nameWithoutExt = basename(relPath).replace(/\.(mdx?)$/, '');
-            // Use 'doc' suffix to avoid collision with the 'file'-suffixed File node
-            const docId = makeId(relPath.replace(/\//g, '_'), 'doc');
+            // Use the 'doc' kind to avoid collision with the 'file'-kinded File node
+            const relDocId = docId(relPath);
             const docNode = {
-                id: docId,
+                id: relDocId,
                 label: 'Document',
                 name: nameWithoutExt,
                 normLabel: toNormLabel(nameWithoutExt),
@@ -65,10 +65,10 @@ export const markdownPhase = {
                     // Exact name match, excluding structural nodes to avoid matching file names
                     const rows = symbolLookup.all(span);
                     if (rows.length === 1) {
-                        const edgeId = makeId(docId, rows[0].id, 'references');
+                        const edgeId = makeId(relDocId, rows[0].id, 'references');
                         referencesEdges.push({
                             id: edgeId,
-                            sourceId: docId,
+                            sourceId: relDocId,
                             targetId: rows[0].id,
                             relation: 'REFERENCES',
                             confidence: 'INFERRED',

package/dist/src/pipeline/phases/markdown.js.map

@@ -1 +1 @@
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+{"version":3,"file":"markdown.js","sourceRoot":"","sources":["../../../../src/pipeline/phases/markdown.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,YAAY,EAAE,QAAQ,EAAE,MAAM,SAAS,CAAC;AACjD,OAAO,EAAE,QAAQ,EAAE,OAAO,EAAE,MAAM,WAAW,CAAC;AAC9C,OAAO,EAAE,WAAW,EAAE,MAAM,6BAA6B,CAAC;AAC1D,OAAO,EAAE,WAAW,EAAE,MAAM,6BAA6B,CAAC;AAE1D,OAAO,EAAE,KAAK,EAAE,MAAM,EAAE,WAAW,EAAE,MAAM,gBAAgB,CAAC;AAI5D,MAAM,mBAAmB,GAAG,IAAI,GAAG,CAAC,CAAC,KAAK,EAAE,MAAM,CAAC,CAAC,CAAC;AACrD,iCAAiC;AACjC,MAAM,cAAc,GAAG,YAAY,CAAC;AACpC,iFAAiF;AACjF,MAAM,aAAa,GAAG,8BAA8B,CAAC;AAOrD,MAAM,CAAC,MAAM,aAAa,GAAkC;IAC1D,IAAI,EAAE,UAAU;IAChB,yEAAyE;IACzE,2DAA2D;IAC3D,6EAA6E;IAC7E,IAAI,EAAE,CAAC,OAAO,EAAE,WAAW,CAAC;IAC5B,KAAK,CAAC,OAAO,CAAC,GAAG,EAAE,IAAI;QACrB,IAAI,GAAG,CAAC,OAAO,CAAC,QAAQ;YAAE,OAAO,EAAE,aAAa,EAAE,EAAE,EAAE,eAAe,EAAE,EAAE,EAAE,CAAC;QAC5E,MAAM,EAAE,SAAS,EAAE,GAAG,IAAI,CAAC,GAAG,CAAC,WAAW,CAAoB,CAAC;QAC/D,MAAM,aAAa,GAAoB,EAAE,CAAC;QAC1C,MAAM,eAAe,GAAoB,EAAE,CAAC;QAE5C,MAAM,OAAO,GAAG,SAAS,CAAC,MAAM,CAAC,CAAC,EAAE,EAAE,EAAE;YACtC,MAAM,GAAG,GAAG,OAAO,CAAC,EAAE,CAAC,IAAI,CAAC,CAAC,WAAW,EAAE,CAAC;YAC3C,OAAO,mBAAmB,CAAC,GAAG,CAAC,GAAG,CAAC,CAAC;QACtC,CAAC,CAAC,CAAC;QAEH,KAAK,MAAM,QAAQ,IAAI,OAAO,EAAE,CAAC;YAC/B,gEAAgE;YAChE,MAAM,OAAO,GAAG,QAAQ,CAAC,QAAQ,IAAI,EAAE,CAAC;YACxC,MAAM,OAAO,GAAG,GAAG,GAAG,CAAC,QAAQ,IAAI,OAAO,EAAE,CAAC;YAE7C,IAAI,MAAc,CAAC;YACnB,IAAI,CAAC;gBACH,MAAM,IAAI,GAAG,QAAQ,CAAC,OAAO,CAAC,CAAC;gBAC/B,IAAI,IAAI,CAAC,IAAI,GAAG,GAAG,CAAC,OAAO,CAAC,gBAAgB;oBAAE,SAAS;gBACvD,MAAM,GAAG,YAAY,CAAC,OAAO,EAAE,OAAO,CAAC,CAAC;YAC1C,CAAC;YAAC,MAAM,CAAC;gBACP,SAAS;YACX,CAAC;YAED,MAAM,cAAc,GAAG,QAAQ,CAAC,OAAO,CAAC,CAAC,OAAO,CAAC,WAAW,EAAE,EAAE,CAAC,CAAC;YAClE,yEAAyE;YACzE,MAAM,QAAQ,GAAG,KAAK,CAAC,OAAO,CAAC,CAAC;YAEhC,MAAM,OAAO,GAAkB;gBAC7B,EAAE,EAAE,QAAQ;gBACZ,KAAK,EAAE,UAAU;gBACjB,IAAI,EAAE,cAAc;gBACpB,SAAS,EAAE,WAAW,CAAC,cAAc,CAAC;gBACtC,QAAQ,EAAE,OAAO;gBACjB,UAAU,EAAE,KAAK;gBACjB,QAAQ,EAAE,UAAU;aACrB,CAAC;YACF,aAAa,CAAC,IAAI,CAAC,OAAO,CAAC,CAAC;YAE5B,qEAAqE;YACrE,IAAI,GAAG,CAAC,EAAE,EAAE,CAAC;gBACX,MAAM,KAAK,GAAG,gBAAgB,CAAC,MAAM,CAAC,CAAC;gBACvC,2EAA2E;gBAC3E,2EAA2E;gBAC3E,MAAM,YAAY,GAAG,GAAG,CAAC,EAAE,CAAC,OAAO,CACjC;2DACiD,CAClD,CAAC;gBAEF,KAAK,MAAM,IAAI,IAAI,KAAK,EAAE,CAAC;oBACzB,uEAAuE;oBACvE,IAAI,CAAC,YAAY,CAAC,IAAI,CAAC;wBAAE,SAAS;oBAElC,4EAA4E;oBAC5E,MAAM,IAAI,GAAG,YAAY,CAAC,GAAG,CAAC,IAAI,CAAqB,CAAC;oBAExD,IAAI,IAAI,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;wBACtB,MAAM,MAAM,GAAG,MAAM,CAAC,QAAQ,EAAE,IAAI,CAAC,CAAC,CAAC,CAAC,EAAE,EAAE,YAAY,CAAC,CAAC;wBAC1D,eAAe,CAAC,IAAI,CAAC;4BACnB,EAAE,EAAE,MAAM;4BACV,QAAQ,EAAE,QAAQ;4BAClB,QAAQ,EAAE,IAAI,CAAC,CAAC,CAAC,CAAC,EAAE;4BACpB,QAAQ,EAAE,YAAY;4BACtB,UAAU,EAAE,UAAU;4BACtB,0EAA0E;4BAC1E,gFAAgF;4BAChF,eAAe,EAAE,GAAG;yBACrB,CAAC,CAAC;oBACL,CAAC;gBACH,CAAC;YACH,CAAC;QACH,CAAC;QAED,IAAI,GAAG,CAAC,EAAE,EAAE,CAAC;YACX,WAAW,CAAC,GAAG,CAAC,EAAE,EAAE,aAAa,CAAC,CAAC;YACnC,WAAW,CAAC,GAAG,CAAC,EAAE,EAAE,eAAe,CAAC,CAAC;QACvC,CAAC;QAED,OAAO,EAAE,aAAa,EAAE,eAAe,EAAE,CAAC;IAC5C,CAAC;CACF,CAAC;AAEF,SAAS,gBAAgB,CAAC,MAAc;IACtC,MAAM,KAAK,GAAa,EAAE,CAAC;IAC3B,IAAI,KAA6B,CAAC;IAClC,MAAM,EAAE,GAAG,IAAI,MAAM,CAAC,cAAc,CAAC,MAAM,EAAE,GAAG,CAAC,CAAC;IAClD,OAAO,CAAC,KAAK,GAAG,EAAE,CAAC,IAAI,CAAC,MAAM,CAAC,CAAC,KAAK,IAAI,EAAE,CAAC;QAC1C,KAAK,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,IAAI,EAAE,CAAC,CAAC;IAC9B,CAAC;IACD,OAAO,KAAK,CAAC;AACf,CAAC;AAED,2GAA2G;AAC3G,SAAS,YAAY,CAAC,IAAY;IAChC,OAAO,aAAa,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC;AAClC,CAAC"}

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

@@ -1 +1 @@
-{"version":3,"file":"parse.d.ts","sourceRoot":"","sources":["../../../../src/pipeline/phases/parse.ts"],"names":[],"mappings":"AAMA,OAAO,KAAK,EAAE,aAAa,EAAE,aAAa,EAAE,MAAM,gBAAgB,CAAC;AACnE,OAAO,KAAK,EAAE,aAAa,EAAE,MAAM,aAAa,CAAC;AAIjD,MAAM,WAAW,WAAW;IAC1B,WAAW,EAAE,aAAa,EAAE,CAAC;IAC7B,QAAQ,EAAE,aAAa,EAAE,CAAC;IAC1B,WAAW,EAAE,MAAM,EAAE,CAAC;IACtB,YAAY,EAAE,GAAG,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC;IAClC,UAAU,EAAE;QAAE,IAAI,EAAE,MAAM,CAAC;QAAC,MAAM,EAAE,MAAM,CAAA;KAAE,CAAC;CAC9C;AAED,eAAO,MAAM,UAAU,EAAE,aAAa,CAAC,WAAW,CAoLjD,CAAC;AAEF,wBAAgB,uBAAuB,CACrC,MAAM,EAAE,MAAM,EACd,QAAQ,EAAE,MAAM,GACf,KAAK,CAAC;IAAE,IAAI,EAAE,MAAM,CAAC;IAAC,KAAK,EAAE,WAAW,CAAC;IAAC,QAAQ,EAAE,MAAM,CAAC;IAAC,IAAI,EAAE,MAAM,CAAA;CAAE,CAAC,CAU7E;AAED,wBAAgB,qBAAqB,CACnC,MAAM,EAAE,MAAM,EACd,QAAQ,EAAE,MAAM,GACf,KAAK,CAAC;IAAE,IAAI,EAAE,MAAM,CAAC;IAAC,UAAU,EAAE,OAAO,CAAC;IAAC,IAAI,EAAE,MAAM,CAAC;IAAC,QAAQ,EAAE,MAAM,CAAA;CAAE,CAAC,CAmB9E"}
+{"version":3,"file":"parse.d.ts","sourceRoot":"","sources":["../../../../src/pipeline/phases/parse.ts"],"names":[],"mappings":"AAMA,OAAO,KAAK,EAAE,aAAa,EAAE,aAAa,EAAE,MAAM,gBAAgB,CAAC;AAEnE,OAAO,KAAK,EAAE,aAAa,EAAE,MAAM,aAAa,CAAC;AAIjD,MAAM,WAAW,WAAW;IAC1B,WAAW,EAAE,aAAa,EAAE,CAAC;IAC7B,QAAQ,EAAE,aAAa,EAAE,CAAC;IAC1B,WAAW,EAAE,MAAM,EAAE,CAAC;IACtB,YAAY,EAAE,GAAG,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC;IAClC,UAAU,EAAE;QAAE,IAAI,EAAE,MAAM,CAAC;QAAC,MAAM,EAAE,MAAM,CAAA;KAAE,CAAC;CAC9C;AAED,eAAO,MAAM,UAAU,EAAE,aAAa,CAAC,WAAW,CA4KjD,CAAC;AAEF,wBAAgB,uBAAuB,CACrC,MAAM,EAAE,MAAM,EACd,QAAQ,EAAE,MAAM,GACf,KAAK,CAAC;IAAE,IAAI,EAAE,MAAM,CAAC;IAAC,KAAK,EAAE,WAAW,CAAC;IAAC,QAAQ,EAAE,MAAM,CAAC;IAAC,IAAI,EAAE,MAAM,CAAA;CAAE,CAAC,CAU7E;AAED,wBAAgB,qBAAqB,CACnC,MAAM,EAAE,MAAM,EACd,QAAQ,EAAE,MAAM,GACf,KAAK,CAAC;IAAE,IAAI,EAAE,MAAM,CAAC;IAAC,UAAU,EAAE,OAAO,CAAC;IAAC,IAAI,EAAE,MAAM,CAAC;IAAC,QAAQ,EAAE,MAAM,CAAA;CAAE,CAAC,CAmB9E"}

package/dist/src/pipeline/phases/parse.js

@@ -4,6 +4,7 @@ import { ExtractionCache } from '../../cache/extraction-cache.js';
 import { parseFile } from '../../parsers/loader.js';
 import { deleteEdgesForFile, insertEdges } from '../../storage/edge-store.js';
 import { deleteNodesForFile, insertNodes } from '../../storage/node-store.js';
+import { symbolId } from '../../types.js';
 import { extractVariables, variableToNode } from './variables.js';
 export const parsePhase = {
     name: 'parse',
@@ -12,17 +13,6 @@ export const parsePhase = {
         const { fileNodes } = deps.get('structure');
         const symbolNodes = [];
         const allEdges = [];
-        // freshNodes/freshEdges (the cache-miss-only subset) are NOT accumulated in a
-        // parallel array during the loop — that duplicated every fresh node/edge object
-        // in memory for the entire pipeline run. Instead we record the [start, end)
-        // slice of symbolNodes/allEdges that each cache-miss file contributed, and
-        // materialize the fresh subset via a single slice pass at the end, only when
-        // it's actually needed (cacheHits > 0). On a cold build (cacheHits === 0) the
-        // fresh subset is never materialized at all, since nodesToInsert falls back to
-        // symbolNodes/allEdges directly in that case — eliminating the redundant
-        // allocation entirely for the memory-heaviest scenario.
-        const freshNodeRanges = [];
-        const freshEdgeRanges = [];
         const staleFilePaths = [];
         const parseErrors = [];
         const fileContents = new Map();
@@ -71,7 +61,12 @@ export const parsePhase = {
                     const csNamespaces = extractCsharpNamespaces(source, fileNode.filePath ?? '');
                     for (const ns of csNamespaces) {
                         fileSymbols.push({
-                            id: `${ns.filePath}::namespace::${ns.name}`,
+                            id: symbolId({
+                                filePath: ns.filePath,
+                                scope: [],
+                                name: ns.name,
+                                kind: 'Namespace',
+                            }),
                             name: ns.name,
                             label: 'Namespace',
                             normLabel: 'namespace',
@@ -87,7 +82,7 @@ export const parsePhase = {
                     const arrowFns = extractArrowFunctions(source, fileNode.filePath ?? '');
                     for (const fn of arrowFns) {
                         fileSymbols.push({
-                            id: `${fn.filePath}::fn::${fn.name}`,
+                            id: symbolId({ filePath: fn.filePath, scope: [], name: fn.name, kind: 'Function' }),
                             name: fn.name,
                             label: 'Function',
                             normLabel: 'function',
@@ -104,12 +99,8 @@ export const parsePhase = {
                 catch {
                     /* non-fatal */
                 }
-                const nodeStart = symbolNodes.length;
-                const edgeStart = allEdges.length;
                 symbolNodes.push(...fileSymbols);
                 allEdges.push(...fileEdges);
-                freshNodeRanges.push([nodeStart, symbolNodes.length]);
-                freshEdgeRanges.push([edgeStart, allEdges.length]);
                 // This file was re-parsed (cache miss) — its OLD node/edge set (from the
                 // previous build) must be deleted before the fresh rows are inserted below,
                 // otherwise a renamed/removed symbol's old row survives forever (ghost rows).
@@ -129,15 +120,20 @@ export const parsePhase = {
         cache.flush();
         if (ctx.db) {
             const db = ctx.db;
-            // Only insert freshly-parsed nodes — cached nodes are already in the DB
-            // from the previous build (node IDs are deterministic from file_path + symbol).
-            // On first build (no cache hits), freshNodes === symbolNodes, so the fresh
-            // subset is never materialized — symbolNodes/allEdges are used directly.
-            const freshNodes = cacheHits > 0 ? freshNodeRanges.flatMap(([s, e]) => symbolNodes.slice(s, e)) : symbolNodes;
-            const freshEdges = cacheHits > 0 ? freshEdgeRanges.flatMap(([s, e]) => allEdges.slice(s, e)) : allEdges;
-            const nodesToInsert = freshNodes;
+            // Insert EVERY extracted node/edge, cache hits included. A cache hit used
+            // to skip insertion on the assumption that those rows were already in
+            // SQLite from a previous build — but the cache is flushed to disk before
+            // the build's SQL transaction commits, so that assumption breaks the
+            // moment the DB and the cache disagree: a build that rolls back (or a
+            // deleted/replaced database file) leaves a fully-populated cache in front
+            // of an empty database, and the next build then "succeeds" with zero
+            // nodes. Treating cached extraction as reusable INPUT that can repopulate
+            // storage on its own keeps the cache a pure parse accelerator instead of
+            // a store that another store's contents silently depend on. Node IDs are
+            // deterministic, so re-inserting an unchanged row is an idempotent upsert.
+            const nodesToInsert = symbolNodes;
             const knownIds = new Set(symbolNodes.map((n) => n.id));
-            const edgesToInsert = freshEdges.filter((e) => knownIds.has(e.targetId));
+            const edgesToInsert = allEdges.filter((e) => knownIds.has(e.targetId));
             // For every cache-miss file, purge its OLD node/edge set BEFORE inserting the
             // fresh parse results, inside the same transaction — otherwise a renamed or
             // removed symbol's old row would survive forever (INSERT OR REPLACE only
@@ -157,12 +153,11 @@ export const parsePhase = {
             ctx.allFilesCached = true;
         }
         if (cacheHits > 0) {
-            const freshNodeCount = freshNodeRanges.reduce((sum, [s, e]) => sum + (e - s), 0);
             ctx.onProgress?.({
                 phase: 'parse',
                 filesProcessed: processed,
                 totalFiles: fileNodes.length,
-                message: `cache: ${cacheHits} hits, ${cacheMisses} misses (${freshNodeCount} nodes inserted)`,
+                message: `cache: ${cacheHits} hits, ${cacheMisses} misses (${symbolNodes.length} nodes inserted)`,
             });
         }
         return {

package/dist/src/pipeline/phases/parse.js.map

@@ -1 +1 @@
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+{"version":3,"file":"parse.js","sourceRoot":"","sources":["../../../../src/pipeline/phases/parse.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,YAAY,EAAE,QAAQ,EAAE,MAAM,SAAS,CAAC;AACjD,OAAO,EAAE,OAAO,EAAE,IAAI,EAAE,MAAM,WAAW,CAAC;AAC1C,OAAO,EAAE,eAAe,EAAE,MAAM,iCAAiC,CAAC;AAClE,OAAO,EAAE,SAAS,EAAE,MAAM,yBAAyB,CAAC;AACpD,OAAO,EAAE,kBAAkB,EAAE,WAAW,EAAE,MAAM,6BAA6B,CAAC;AAC9E,OAAO,EAAE,kBAAkB,EAAE,WAAW,EAAE,MAAM,6BAA6B,CAAC;AAE9E,OAAO,EAAE,QAAQ,EAAE,MAAM,gBAAgB,CAAC;AAG1C,OAAO,EAAE,gBAAgB,EAAE,cAAc,EAAE,MAAM,gBAAgB,CAAC;AAUlE,MAAM,CAAC,MAAM,UAAU,GAA+B;IACpD,IAAI,EAAE,OAAO;IACb,IAAI,EAAE,CAAC,WAAW,CAAC;IACnB,KAAK,CAAC,OAAO,CAAC,GAAG,EAAE,IAAI;QACrB,MAAM,EAAE,SAAS,EAAE,GAAG,IAAI,CAAC,GAAG,CAAC,WAAW,CAAoB,CAAC;QAC/D,MAAM,WAAW,GAAoB,EAAE,CAAC;QACxC,MAAM,QAAQ,GAAoB,EAAE,CAAC;QACrC,MAAM,cAAc,GAAa,EAAE,CAAC;QACpC,MAAM,WAAW,GAAa,EAAE,CAAC;QACjC,MAAM,YAAY,GAAG,IAAI,GAAG,EAAkB,CAAC;QAC/C,IAAI,SAAS,GAAG,CAAC,CAAC;QAClB,IAAI,SAAS,GAAG,CAAC,CAAC;QAClB,IAAI,WAAW,GAAG,CAAC,CAAC;QAEpB,MAAM,KAAK,GAAG,IAAI,eAAe,CAAC,IAAI,CAAC,GAAG,CAAC,QAAQ,EAAE,WAAW,EAAE,aAAa,CAAC,CAAC,CAAC;QAElF,KAAK,MAAM,QAAQ,IAAI,SAAS,EAAE,CAAC;YACjC,MAAM,OAAO,GAAG,QAAQ,CAAC,QAAQ,CAAC,CAAC,CAAC,GAAG,GAAG,CAAC,QAAQ,IAAI,QAAQ,CAAC,QAAQ,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC;YAChF,MAAM,GAAG,GAAG,OAAO,CAAC,OAAO,CAAC,CAAC,WAAW,EAAE,CAAC;YAC3C,IAAI,GAAG,KAAK,KAAK,IAAI,GAAG,KAAK,WAAW,EAAE,CAAC;gBACzC,SAAS,EAAE,CAAC;gBACZ,SAAS;YACX,CAAC;YAED,oEAAoE;YACpE,8EAA8E;YAC9E,wEAAwE;YACxE,MAAM,MAAM,GAAG,GAAG,CAAC,OAAO,CAAC,KAAK,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,KAAK,CAAC,WAAW,CAAC,OAAO,CAAC,CAAC;YACrE,IAAI,MAAM,EAAE,CAAC;gBACX,WAAW,CAAC,IAAI,CAAC,GAAG,MAAM,CAAC,KAAK,CAAC,CAAC;gBAClC,QAAQ,CAAC,IAAI,CAAC,GAAG,MAAM,CAAC,KAAK,CAAC,CAAC;gBAC/B,SAAS,EAAE,CAAC;YACd,CAAC;iBAAM,CAAC;gBACN,IAAI,MAAc,CAAC;gBACnB,IAAI,CAAC;oBACH,MAAM,IAAI,GAAG,QAAQ,CAAC,OAAO,CAAC,CAAC;oBAC/B,IAAI,IAAI,CAAC,IAAI,GAAG,GAAG,CAAC,OAAO,CAAC,gBAAgB,EAAE,CAAC;wBAC7C,WAAW,CAAC,IAAI,CAAC,GAAG,QAAQ,CAAC,QAAQ,uBAAuB,CAAC,CAAC;wBAC9D,SAAS;oBACX,CAAC;oBACD,MAAM,GAAG,YAAY,CAAC,OAAO,EAAE,OAAO,CAAC,CAAC;gBAC1C,CAAC;gBAAC,OAAO,GAAG,EAAE,CAAC;oBACb,MAAM,IAAI,GAAI,GAA6B,EAAE,IAAI,CAAC;oBAClD,MAAM,MAAM,GAAG,IAAI,IAAI,CAAC,GAAG,YAAY,KAAK,CAAC,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC,CAAC,CAAC,MAAM,CAAC,GAAG,CAAC,CAAC,CAAC;oBAC1E,WAAW,CAAC,IAAI,CAAC,GAAG,QAAQ,CAAC,QAAQ,iBAAiB,MAAM,GAAG,CAAC,CAAC;oBACjE,SAAS;gBACX,CAAC;gBACD,YAAY,CAAC,GAAG,CAAC,QAAQ,CAAC,QAAQ,IAAI,OAAO,EAAE,MAAM,CAAC,CAAC;gBACvD,MAAM,MAAM,GAAG,MAAM,SAAS,CAAC,OAAO,EAAE,MAAM,EAAE,QAAQ,CAAC,QAAQ,IAAI,EAAE,CAAC,CAAC;gBACzE,MAAM,WAAW,GAAoB,CAAC,GAAG,MAAM,CAAC,KAAK,CAAC,CAAC;gBACvD,MAAM,SAAS,GAAoB,CAAC,GAAG,MAAM,CAAC,KAAK,CAAC,CAAC;gBACrD,WAAW,CAAC,IAAI,CAAC,GAAG,MAAM,CAAC,WAAW,CAAC,CAAC;gBAExC,IAAI,GAAG,KAAK,KAAK,EAAE,CAAC;oBAClB,MAAM,YAAY,GAAG,uBAAuB,CAAC,MAAM,EAAE,QAAQ,CAAC,QAAQ,IAAI,EAAE,CAAC,CAAC;oBAC9E,KAAK,MAAM,EAAE,IAAI,YAAY,EAAE,CAAC;wBAC9B,WAAW,CAAC,IAAI,CAAC;4BACf,EAAE,EAAE,QAAQ,CAAC;gCACX,QAAQ,EAAE,EAAE,CAAC,QAAQ;gCACrB,KAAK,EAAE,EAAE;gCACT,IAAI,EAAE,EAAE,CAAC,IAAI;gCACb,IAAI,EAAE,WAAW;6BAClB,CAAC;4BACF,IAAI,EAAE,EAAE,CAAC,IAAI;4BACb,KAAK,EAAE,WAAW;4BAClB,SAAS,EAAE,WAAW;4BACtB,QAAQ,EAAE,EAAE,CAAC,QAAQ;4BACrB,IAAI,EAAE,EAAE,CAAC,IAAI;4BACb,UAAU,EAAE,IAAI;yBACyB,CAAC,CAAC;oBAC/C,CAAC;gBACH,CAAC;gBAED,IAAI,CAAC,KAAK,EAAE,MAAM,EAAE,KAAK,EAAE,MAAM,CAAC,CAAC,QAAQ,CAAC,GAAG,CAAC,EAAE,CAAC;oBACjD,MAAM,QAAQ,GAAG,gBAAgB,CAAC,MAAM,EAAE,QAAQ,CAAC,QAAQ,IAAI,EAAE,CAAC,CAAC;oBACnE,WAAW,CAAC,IAAI,CAAC,GAAG,QAAQ,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,cAAc,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC;oBAE5D,MAAM,QAAQ,GAAG,qBAAqB,CAAC,MAAM,EAAE,QAAQ,CAAC,QAAQ,IAAI,EAAE,CAAC,CAAC;oBACxE,KAAK,MAAM,EAAE,IAAI,QAAQ,EAAE,CAAC;wBAC1B,WAAW,CAAC,IAAI,CAAC;4BACf,EAAE,EAAE,QAAQ,CAAC,EAAE,QAAQ,EAAE,EAAE,CAAC,QAAQ,EAAE,KAAK,EAAE,EAAE,EAAE,IAAI,EAAE,EAAE,CAAC,IAAI,EAAE,IAAI,EAAE,UAAU,EAAE,CAAC;4BACnF,IAAI,EAAE,EAAE,CAAC,IAAI;4BACb,KAAK,EAAE,UAAU;4BACjB,SAAS,EAAE,UAAU;4BACrB,QAAQ,EAAE,EAAE,CAAC,QAAQ;4BACrB,IAAI,EAAE,EAAE,CAAC,IAAI;4BACb,UAAU,EAAE,EAAE,CAAC,UAAU;yBACgB,CAAC,CAAC;oBAC/C,CAAC;gBACH,CAAC;gBAED,IAAI,CAAC;oBACH,MAAM,QAAQ,GAAG,KAAK,CAAC,WAAW,CAAC,MAAM,CAAC,CAAC;oBAC3C,KAAK,CAAC,WAAW,CAAC,OAAO,EAAE,QAAQ,EAAE,WAAW,EAAE,SAAS,CAAC,CAAC;gBAC/D,CAAC;gBAAC,MAAM,CAAC;oBACP,eAAe;gBACjB,CAAC;gBACD,WAAW,CAAC,IAAI,CAAC,GAAG,WAAW,CAAC,CAAC;gBACjC,QAAQ,CAAC,IAAI,CAAC,GAAG,SAAS,CAAC,CAAC;gBAC5B,yEAAyE;gBACzE,4EAA4E;gBAC5E,8EAA8E;gBAC9E,IAAI,QAAQ,CAAC,QAAQ;oBAAE,cAAc,CAAC,IAAI,CAAC,QAAQ,CAAC,QAAQ,CAAC,CAAC;gBAC9D,WAAW,EAAE,CAAC;YAChB,CAAC;YACD,SAAS,EAAE,CAAC;YAEZ,IAAI,SAAS,GAAG,EAAE,KAAK,CAAC,EAAE,CAAC;gBACzB,GAAG,CAAC,UAAU,EAAE,CAAC;oBACf,KAAK,EAAE,OAAO;oBACd,cAAc,EAAE,SAAS;oBACzB,UAAU,EAAE,SAAS,CAAC,MAAM;iBAC7B,CAAC,CAAC;YACL,CAAC;QACH,CAAC;QAED,KAAK,CAAC,KAAK,EAAE,CAAC;QAEd,IAAI,GAAG,CAAC,EAAE,EAAE,CAAC;YACX,MAAM,EAAE,GAAG,GAAG,CAAC,EAAE,CAAC;YAClB,0EAA0E;YAC1E,sEAAsE;YACtE,yEAAyE;YACzE,qEAAqE;YACrE,sEAAsE;YACtE,0EAA0E;YAC1E,qEAAqE;YACrE,0EAA0E;YAC1E,yEAAyE;YACzE,yEAAyE;YACzE,2EAA2E;YAC3E,MAAM,aAAa,GAAG,WAAW,CAAC;YAClC,MAAM,QAAQ,GAAG,IAAI,GAAG,CAAC,WAAW,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC;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package/dist/src/pipeline/phases/pdf-parse.js

@@ -2,7 +2,7 @@ import { readdirSync, readFileSync, statSync } from 'node:fs';
 import { basename, extname, join, relative } from 'node:path';
 import { insertEdges } from '../../storage/edge-store.js';
 import { insertNodes } from '../../storage/node-store.js';
-import { CONFIDENCE_SCORE, makeId, toNormLabel } from '../../types.js';
+import { CONFIDENCE_SCORE, fileId, makeId, toNormLabel } from '../../types.js';
 const IGNORE_DIRS = new Set([
     'node_modules',
     '.git',
@@ -76,7 +76,7 @@ export const pdfParsePhase = {
         const allEdges = [];
         for (const absPath of pdfPaths) {
             const rel = relative(ctx.repoPath, absPath);
-            const fileId = makeId(rel.replace(/\//g, '_'), 'file');
+            const relFileId = fileId(rel);
             let text;
             try {
                 const buf = readFileSync(absPath);
@@ -101,7 +101,7 @@ export const pdfParsePhase = {
             for (let i = 0; i < chunks.length; i++) {
                 const { content, startChar } = chunks[i];
                 const title = `${docTitle} §${i + 1}`;
-                const sectionId = makeId('section', fileId, String(i));
+                const sectionId = makeId('section', relFileId, String(i));
                 const node = {
                     id: sectionId,
                     label: 'Section',
@@ -115,8 +115,8 @@ export const pdfParsePhase = {
                 };
                 sectionNodes.push(node);
                 allEdges.push({
-                    id: makeId(fileId, sectionId, 'defines'),
-                    sourceId: fileId,
+                    id: makeId(relFileId, sectionId, 'defines'),
+                    sourceId: relFileId,
                     targetId: sectionId,
                     relation: 'DEFINES',
                     confidence: 'EXTRACTED',

package/dist/src/pipeline/phases/pdf-parse.js.map

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

@@ -1 +1 @@
-{"version":3,"file":"scan.d.ts","sourceRoot":"","sources":["../../../../src/pipeline/phases/scan.ts"],"names":[],"mappings":"AAKA,OAAO,KAAK,EAAE,aAAa,EAAE,MAAM,aAAa,CAAC;AA+CjD,MAAM,WAAW,UAAU;IACzB,SAAS,EAAE,MAAM,EAAE,CAAC;IACpB,UAAU,EAAE,MAAM,CAAC;CACpB;AAED,eAAO,MAAM,SAAS,EAAE,aAAa,CAAC,UAAU,CAiG/C,CAAC;AAEF,MAAM,WAAW,gBAAgB;IAC/B,KAAK,EAAE,IAAI,GAAG,MAAM,GAAG,MAAM,CAAC;IAC9B,OAAO,EAAE,MAAM,CAAC;CACjB;AAOD,wBAAgB,YAAY,CAAC,IAAI,EAAE;IAAE,SAAS,EAAE,MAAM,CAAC;IAAC,UAAU,EAAE,MAAM,CAAA;CAAE,GAAG,gBAAgB,CAe9F"}
+{"version":3,"file":"scan.d.ts","sourceRoot":"","sources":["../../../../src/pipeline/phases/scan.ts"],"names":[],"mappings":"AAKA,OAAO,KAAK,EAAE,aAAa,EAAE,MAAM,aAAa,CAAC;AA8DjD,MAAM,WAAW,UAAU;IACzB,SAAS,EAAE,MAAM,EAAE,CAAC;IACpB,UAAU,EAAE,MAAM,CAAC;CACpB;AAED,eAAO,MAAM,SAAS,EAAE,aAAa,CAAC,UAAU,CAiG/C,CAAC;AAEF,MAAM,WAAW,gBAAgB;IAC/B,KAAK,EAAE,IAAI,GAAG,MAAM,GAAG,MAAM,CAAC;IAC9B,OAAO,EAAE,MAAM,CAAC;CACjB;AAOD,wBAAgB,YAAY,CAAC,IAAI,EAAE;IAAE,SAAS,EAAE,MAAM,CAAC;IAAC,UAAU,EAAE,MAAM,CAAA;CAAE,GAAG,gBAAgB,CAe9F"}

package/dist/src/pipeline/phases/scan.js

@@ -19,6 +19,13 @@ const DEFAULT_IGNORE = new Set([
     '.claude-plugin',
     '.github',
     '.githooks',
+    '.next',
+    '.nuxt',
+    '.svelte-kit',
+    '.turbo',
+    '.vercel',
+    '.wrangler',
+    '.open-next',
 ]);
 const BINARY_EXTENSIONS = new Set([
     '.png',
@@ -44,7 +51,15 @@ const BINARY_EXTENSIONS = new Set([
     '.class',
     '.jar',
 ]);
-const GENERATED_PATTERNS = [/\.min\.(js|css)$/, /\.pb\.go$/, /_generated\.ts$/];
+const GENERATED_PATTERNS = [
+    /\.min\.(js|css)$/,
+    /\.pb\.go$/,
+    /_generated\.ts$/,
+    // Monograph's own build output (reporting/graph-report.ts writes it to the repo
+    // root). Indexing it feeds a previous build's prose back into the graph as
+    // document nodes and edges, compounding on every rebuild.
+    /^GRAPH_REPORT\.md$/,
+];
 export const scanPhase = {
     name: 'scan',
     deps: [],

package/dist/src/pipeline/phases/scan.js.map

@@ -1 +1 @@
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package/dist/src/pipeline/phases/structure.js

@@ -1,5 +1,5 @@
 import { basename, dirname, relative } from 'node:path';
-import { CONFIDENCE_SCORE, makeId, toNormLabel } from '../../types.js';
+import { CONFIDENCE_SCORE, fileId, folderId, makeId, toNormLabel } from '../../types.js';
 export const structurePhase = {
     name: 'structure',
     deps: ['scan'],
@@ -11,9 +11,9 @@ export const structurePhase = {
         const seenFolders = new Set();
         for (const absPath of filePaths) {
             const rel = relative(ctx.repoPath, absPath);
-            const fileId = makeId(rel.replace(/\//g, '_'), 'file');
+            const relFileId = fileId(rel);
             fileNodes.push({
-                id: fileId,
+                id: relFileId,
                 label: 'File',
                 name: basename(rel),
                 normLabel: toNormLabel(basename(rel)),
@@ -27,11 +27,11 @@ export const structurePhase = {
                 if (part === '.')
                     continue;
                 current = current ? `${current}/${part}` : part;
-                const folderId = makeId(current.replace(/\//g, '_'), 'folder');
-                if (!seenFolders.has(folderId)) {
-                    seenFolders.add(folderId);
+                const currentFolderId = folderId(current);
+                if (!seenFolders.has(currentFolderId)) {
+                    seenFolders.add(currentFolderId);
                     folderNodes.push({
-                        id: folderId,
+                        id: currentFolderId,
                         label: 'Folder',
                         name: part,
                         normLabel: toNormLabel(part),
@@ -40,22 +40,22 @@ export const structurePhase = {
                     });
                     if (parentFolderId) {
                         containsEdges.push({
-                            id: makeId(parentFolderId, folderId, 'contains'),
+                            id: makeId(parentFolderId, currentFolderId, 'contains'),
                             sourceId: parentFolderId,
-                            targetId: folderId,
+                            targetId: currentFolderId,
                             relation: 'CONTAINS',
                             confidence: 'EXTRACTED',
                             confidenceScore: CONFIDENCE_SCORE.EXTRACTED,
                         });
                     }
                 }
-                parentFolderId = folderId;
+                parentFolderId = currentFolderId;
             }
             if (parentFolderId) {
                 containsEdges.push({
-                    id: makeId(parentFolderId, fileId, 'contains'),
+                    id: makeId(parentFolderId, relFileId, 'contains'),
                     sourceId: parentFolderId,
-                    targetId: fileId,
+                    targetId: relFileId,
                     relation: 'CONTAINS',
                     confidence: 'EXTRACTED',
                     confidenceScore: CONFIDENCE_SCORE.EXTRACTED,