fix: close edge gap in watcher's single-file rebuild (#533)

rebuildFile (used by watch mode) deleted all edges for a changed file
but only rebuilt the file's own outgoing edges — incoming edges from
other files were lost. This produced ~3.3% fewer edges than a full build.

Root causes fixed:
- No reverse-dep cascade: files importing the changed file never had
  their outgoing edges rebuilt after the changed file's node IDs changed.
  Added findReverseDeps + two-pass rebuild (direct edges first, then
  barrel resolution) to match the build pipeline's behavior.
- Missing child nodes: insertFileNodes skipped def.children (parameters,
  properties), losing contains/parameter_of edges.
- Missing containment edges: file→symbol and dir→file contains edges
  were never created by the watcher path.
- Missing ancillary table cleanup: function_complexity, cfg_blocks, etc.
  had FK references to old nodes, causing SQLITE_CONSTRAINT_FOREIGNKEY
  on node deletion. Added purgeAncillaryData before node deletion.
- No barrel resolution: import edges through re-export chains (barrel
  files) were not resolved, losing transitive import edges.

Author: carlos-alm

src/domain/graph/builder/incremental.js

@@ -3,9 +3,13 @@
  *
  * Reuses pipeline helpers instead of duplicating node insertion and edge building
  * logic from the main builder. This eliminates the watcher.js divergence (ROADMAP 3.9).
+ *
+ * Reverse-dep cascade: when a file changes, files that have edges targeting it
+ * must have their outgoing edges rebuilt (since the changed file's node IDs change).
  */
 import fs from 'node:fs';
 import path from 'node:path';
+import { bulkNodeIdsByFile } from '../../../db/index.js';
 import { warn } from '../../../infrastructure/logger.js';
 import { normalizePath } from '../../../shared/constants.js';
 import { parseFileIncremental } from '../../parser.js';
@@ -18,15 +22,204 @@ function insertFileNodes(stmts, relPath, symbols) {
   stmts.insertNode.run(relPath, 'file', relPath, 0, null);
   for (const def of symbols.definitions) {
     stmts.insertNode.run(def.name, def.kind, relPath, def.line, def.endLine || null);
+    if (def.children?.length) {
+      for (const child of def.children) {
+        stmts.insertNode.run(
+          child.name,
+          child.kind,
+          relPath,
+          child.line,
+          child.endLine || null,
+        );
+      }
+    }
   }
   for (const exp of symbols.exports) {
     stmts.insertNode.run(exp.name, exp.kind, relPath, exp.line, null);
   }
 }
 
+// ── Containment edges ──────────────────────────────────────────────────
+
+function buildContainmentEdges(db, stmts, relPath, symbols) {
+  const nodeIdMap = new Map();
+  for (const row of bulkNodeIdsByFile(db, relPath)) {
+    nodeIdMap.set(`${row.name}|${row.kind}|${row.line}`, row.id);
+  }
+  const fileId = nodeIdMap.get(`${relPath}|file|0`);
+  let edgesAdded = 0;
+  for (const def of symbols.definitions) {
+    const defId = nodeIdMap.get(`${def.name}|${def.kind}|${def.line}`);
+    if (fileId && defId) {
+      stmts.insertEdge.run(fileId, defId, 'contains', 1.0, 0);
+      edgesAdded++;
+    }
+    if (def.children?.length && defId) {
+      for (const child of def.children) {
+        const childId = nodeIdMap.get(`${child.name}|${child.kind}|${child.line}`);
+        if (childId) {
+          stmts.insertEdge.run(defId, childId, 'contains', 1.0, 0);
+          edgesAdded++;
+          if (child.kind === 'parameter') {
+            stmts.insertEdge.run(childId, defId, 'parameter_of', 1.0, 0);
+            edgesAdded++;
+          }
+        }
+      }
+    }
+  }
+  return edgesAdded;
+}
+
+// ── Reverse-dep cascade ────────────────────────────────────────────────
+
+function findReverseDeps(db, relPath) {
+  return db
+    .prepare(
+      `SELECT DISTINCT n_src.file FROM edges e
+       JOIN nodes n_src ON e.source_id = n_src.id
+       JOIN nodes n_tgt ON e.target_id = n_tgt.id
+       WHERE n_tgt.file = ? AND n_src.file != ? AND n_src.kind != 'directory'`,
+    )
+    .all(relPath, relPath)
+    .map((r) => r.file);
+}
+
+function deleteOutgoingEdges(db, relPath) {
+  db.prepare('DELETE FROM edges WHERE source_id IN (SELECT id FROM nodes WHERE file = ?)').run(
+    relPath,
+  );
+}
+
+async function parseReverseDep(rootDir, depRelPath, engineOpts, cache) {
+  const absPath = path.join(rootDir, depRelPath);
+  if (!fs.existsSync(absPath)) return null;
+
+  let code;
+  try {
+    code = readFileSafe(absPath);
+  } catch {
+    return null;
+  }
+
+  return parseFileIncremental(cache, absPath, code, engineOpts);
+}
+
+function rebuildReverseDepEdges(db, rootDir, depRelPath, symbols, stmts, skipBarrel) {
+  const fileNodeRow = stmts.getNodeId.get(depRelPath, 'file', depRelPath, 0);
+  if (!fileNodeRow) return 0;
+
+  const aliases = { baseUrl: null, paths: {} };
+  let edgesAdded = buildContainmentEdges(db, stmts, depRelPath, symbols);
+  // Don't rebuild dir→file containment for reverse-deps (it was never deleted)
+  edgesAdded += buildImportEdges(
+    stmts,
+    depRelPath,
+    symbols,
+    rootDir,
+    fileNodeRow.id,
+    aliases,
+    skipBarrel ? null : db,
+  );
+  const importedNames = buildImportedNamesMap(symbols, rootDir, depRelPath, aliases);
+  edgesAdded += buildCallEdges(stmts, depRelPath, symbols, fileNodeRow, importedNames);
+  return edgesAdded;
+}
+
+// ── Directory containment edges ────────────────────────────────────────
+
+function rebuildDirContainment(db, stmts, relPath) {
+  const dir = normalizePath(path.dirname(relPath));
+  if (!dir || dir === '.') return 0;
+  const dirRow = stmts.getNodeId.get(dir, 'directory', dir, 0);
+  const fileRow = stmts.getNodeId.get(relPath, 'file', relPath, 0);
+  if (dirRow && fileRow) {
+    stmts.insertEdge.run(dirRow.id, fileRow.id, 'contains', 1.0, 0);
+    return 1;
+  }
+  return 0;
+}
+
+// ── Ancillary table cleanup ────────────────────────────────────────────
+
+function purgeAncillaryData(db, relPath) {
+  const tryExec = (sql, ...args) => {
+    try {
+      db.prepare(sql).run(...args);
+    } catch {
+      /* table may not exist */
+    }
+  };
+  tryExec(
+    'DELETE FROM function_complexity WHERE node_id IN (SELECT id FROM nodes WHERE file = ?)',
+    relPath,
+  );
+  tryExec(
+    'DELETE FROM node_metrics WHERE node_id IN (SELECT id FROM nodes WHERE file = ?)',
+    relPath,
+  );
+  tryExec(
+    'DELETE FROM cfg_edges WHERE function_node_id IN (SELECT id FROM nodes WHERE file = ?)',
+    relPath,
+  );
+  tryExec(
+    'DELETE FROM cfg_blocks WHERE function_node_id IN (SELECT id FROM nodes WHERE file = ?)',
+    relPath,
+  );
+  tryExec(
+    'DELETE FROM dataflow WHERE source_id IN (SELECT id FROM nodes WHERE file = ?) OR target_id IN (SELECT id FROM nodes WHERE file = ?)',
+    relPath,
+    relPath,
+  );
+  tryExec('DELETE FROM ast_nodes WHERE file = ?', relPath);
+}
+
 // ── Import edge building ────────────────────────────────────────────────
 
-function buildImportEdges(stmts, relPath, symbols, rootDir, fileNodeId, aliases) {
+function isBarrelFile(db, relPath) {
+  const reexportCount = db
+    .prepare(
+      `SELECT COUNT(*) as c FROM edges e
+       JOIN nodes n ON e.source_id = n.id
+       WHERE e.kind = 'reexports' AND n.file = ? AND n.kind = 'file'`,
+    )
+    .get(relPath)?.c;
+  return (reexportCount || 0) > 0;
+}
+
+function resolveBarrelTarget(db, barrelPath, symbolName, visited = new Set()) {
+  if (visited.has(barrelPath)) return null;
+  visited.add(barrelPath);
+
+  // Find re-export targets from this barrel
+  const reexportTargets = db
+    .prepare(
+      `SELECT DISTINCT n2.file FROM edges e
+       JOIN nodes n1 ON e.source_id = n1.id
+       JOIN nodes n2 ON e.target_id = n2.id
+       WHERE e.kind = 'reexports' AND n1.file = ? AND n1.kind = 'file'`,
+    )
+    .all(barrelPath);
+
+  for (const { file: targetFile } of reexportTargets) {
+    // Check if the symbol is defined in this target file
+    const hasDef = db
+      .prepare(
+        `SELECT 1 FROM nodes WHERE name = ? AND file = ? AND kind != 'file' AND kind != 'directory' LIMIT 1`,
+      )
+      .get(symbolName, targetFile);
+    if (hasDef) return targetFile;
+
+    // Recurse through barrel chains
+    if (isBarrelFile(db, targetFile)) {
+      const deeper = resolveBarrelTarget(db, targetFile, symbolName, visited);
+      if (deeper) return deeper;
+    }
+  }
+  return null;
+}
+
+function buildImportEdges(stmts, relPath, symbols, rootDir, fileNodeId, aliases, db) {
   let edgesAdded = 0;
   for (const imp of symbols.imports) {
     const resolvedPath = resolveImportPath(
@@ -40,6 +233,24 @@ function buildImportEdges(stmts, relPath, symbols, rootDir, fileNodeId, aliases)
       const edgeKind = imp.reexport ? 'reexports' : imp.typeOnly ? 'imports-type' : 'imports';
       stmts.insertEdge.run(fileNodeId, targetRow.id, edgeKind, 1.0, 0);
       edgesAdded++;
+
+      // Barrel resolution: create edges through re-export chains
+      if (!imp.reexport && db && isBarrelFile(db, resolvedPath)) {
+        const resolvedSources = new Set();
+        for (const name of imp.names) {
+          const cleanName = name.replace(/^\*\s+as\s+/, '');
+          const actualSource = resolveBarrelTarget(db, resolvedPath, cleanName);
+          if (actualSource && actualSource !== resolvedPath && !resolvedSources.has(actualSource)) {
+            resolvedSources.add(actualSource);
+            const actualRow = stmts.getNodeId.get(actualSource, 'file', actualSource, 0);
+            if (actualRow) {
+              const kind = edgeKind === 'imports-type' ? 'imports-type' : 'imports';
+              stmts.insertEdge.run(fileNodeId, actualRow.id, kind, 0.9, 0);
+              edgesAdded++;
+            }
+          }
+        }
+      }
     }
   }
   return edgesAdded;
@@ -156,12 +367,17 @@ function buildCallEdges(stmts, relPath, symbols, fileNodeRow, importedNames) {
  * @param {Function} [options.diffSymbols] - Symbol diff function
  * @returns {Promise<object|null>} Update result or null on failure
  */
-export async function rebuildFile(_db, rootDir, filePath, stmts, engineOpts, cache, options = {}) {
+export async function rebuildFile(db, rootDir, filePath, stmts, engineOpts, cache, options = {}) {
   const { diffSymbols } = options;
   const relPath = normalizePath(path.relative(rootDir, filePath));
   const oldNodes = stmts.countNodes.get(relPath)?.c || 0;
   const oldSymbols = diffSymbols ? stmts.listSymbols.all(relPath) : [];
 
+  // Find reverse-deps BEFORE purging (edges still reference the old nodes)
+  const reverseDeps = findReverseDeps(db, relPath);
+
+  // Purge ancillary tables, then edges, then nodes
+  purgeAncillaryData(db, relPath);
   stmts.deleteEdgesForFile.run(relPath);
   stmts.deleteNodes.run(relPath);
 
@@ -203,10 +419,61 @@ export async function rebuildFile(_db, rootDir, filePath, stmts, engineOpts, cac
 
   const aliases = { baseUrl: null, paths: {} };
 
-  let edgesAdded = buildImportEdges(stmts, relPath, symbols, rootDir, fileNodeRow.id, aliases);
+  let edgesAdded = buildContainmentEdges(db, stmts, relPath, symbols);
+  edgesAdded += rebuildDirContainment(db, stmts, relPath);
+  edgesAdded += buildImportEdges(stmts, relPath, symbols, rootDir, fileNodeRow.id, aliases, db);
   const importedNames = buildImportedNamesMap(symbols, rootDir, relPath, aliases);
   edgesAdded += buildCallEdges(stmts, relPath, symbols, fileNodeRow, importedNames);
 
+  // Cascade: rebuild outgoing edges for reverse-dep files.
+  // Two-pass approach: first rebuild direct edges (creating reexports edges for barrels),
+  // then add barrel import edges (which need reexports edges to exist for resolution).
+  const depSymbols = new Map();
+  for (const depRelPath of reverseDeps) {
+    deleteOutgoingEdges(db, depRelPath);
+    const symbols_ = await parseReverseDep(rootDir, depRelPath, engineOpts, cache);
+    if (symbols_) depSymbols.set(depRelPath, symbols_);
+  }
+  // Pass 1: direct edges only (no barrel resolution) — creates reexports edges
+  for (const [depRelPath, symbols_] of depSymbols) {
+    edgesAdded += rebuildReverseDepEdges(db, rootDir, depRelPath, symbols_, stmts, true);
+  }
+  // Pass 2: add barrel import edges (reexports edges now exist)
+  for (const [depRelPath, symbols_] of depSymbols) {
+    const fileNodeRow_ = stmts.getNodeId.get(depRelPath, 'file', depRelPath, 0);
+    if (!fileNodeRow_) continue;
+    const aliases_ = { baseUrl: null, paths: {} };
+    for (const imp of symbols_.imports) {
+      if (imp.reexport) continue;
+      const resolvedPath = resolveImportPath(
+        path.join(rootDir, depRelPath),
+        imp.source,
+        rootDir,
+        aliases_,
+      );
+      if (db && isBarrelFile(db, resolvedPath)) {
+        const resolvedSources = new Set();
+        for (const name of imp.names) {
+          const cleanName = name.replace(/^\*\s+as\s+/, '');
+          const actualSource = resolveBarrelTarget(db, resolvedPath, cleanName);
+          if (
+            actualSource &&
+            actualSource !== resolvedPath &&
+            !resolvedSources.has(actualSource)
+          ) {
+            resolvedSources.add(actualSource);
+            const actualRow = stmts.getNodeId.get(actualSource, 'file', actualSource, 0);
+            if (actualRow) {
+              const kind = imp.typeOnly ? 'imports-type' : 'imports';
+              stmts.insertEdge.run(fileNodeRow_.id, actualRow.id, kind, 0.9, 0);
+              edgesAdded++;
+            }
+          }
+        }
+      }
+    }
+  }
+
   const symbolDiff = diffSymbols ? diffSymbols(oldSymbols, newSymbols) : null;
   const event = oldNodes === 0 ? 'added' : 'modified';
 

tests/fixtures/deep-deps-project/app.js

@@ -0,0 +1,9 @@
+import { runQuery } from './features/query.js';
+import { formatOutput } from './features/format.js';
+import { MAX_ITEMS } from './shared/constants.js';
+
+export function main(input, page) {
+  const results = runQuery(input, page);
+  const label = formatOutput(input);
+  return { label, results, max: MAX_ITEMS };
+}

tests/fixtures/deep-deps-project/domain/index.js

@@ -0,0 +1,2 @@
+export { parseItems } from './parser.js';
+export { resolve } from './resolver.js';

tests/fixtures/deep-deps-project/domain/parser.js

@@ -0,0 +1,6 @@
+import { MAX_ITEMS, clamp } from '../shared/index.js';
+
+export function parseItems(raw) {
+  const items = raw.split(',').map(s => s.trim());
+  return items.slice(0, clamp(items.length, 0, MAX_ITEMS));
+}

tests/fixtures/deep-deps-project/domain/resolver.js

@@ -0,0 +1,7 @@
+import { DEFAULT_NAME } from '../shared/constants.js';
+import { formatName } from '../shared/helpers.js';
+
+export function resolve(input) {
+  const name = input || DEFAULT_NAME;
+  return formatName(name);
+}

tests/fixtures/deep-deps-project/features/format.js

@@ -0,0 +1,7 @@
+import { resolve } from '../domain/resolver.js';
+import { DEFAULT_NAME } from '../shared/index.js';
+
+export function formatOutput(input) {
+  const resolved = resolve(input);
+  return resolved === DEFAULT_NAME ? 'default' : resolved;
+}

tests/fixtures/deep-deps-project/features/query.js

@@ -0,0 +1,9 @@
+import { parseItems } from '../domain/index.js';
+import { paginate } from '../shared/helpers.js';
+import { clamp } from '../shared/constants.js';
+
+export function runQuery(raw, page) {
+  const items = parseItems(raw);
+  const safePage = clamp(page, 0, 100);
+  return paginate(items, safePage, 10);
+}

tests/fixtures/deep-deps-project/shared/constants.js

@@ -0,0 +1,7 @@
+// The deeply-imported leaf file
+export const MAX_ITEMS = 100;
+export const DEFAULT_NAME = 'codegraph';
+
+export function clamp(value, min, max) {
+  return Math.min(Math.max(value, min), max);
+}

tests/fixtures/deep-deps-project/shared/helpers.js

@@ -0,0 +1,11 @@
+import { clamp, MAX_ITEMS } from './constants.js';
+
+export function paginate(items, page, size) {
+  const safeSize = clamp(size, 1, MAX_ITEMS);
+  const start = page * safeSize;
+  return items.slice(start, start + safeSize);
+}
+
+export function formatName(name) {
+  return name.trim().toLowerCase();
+}

tests/fixtures/deep-deps-project/shared/index.js

@@ -0,0 +1,2 @@
+export { MAX_ITEMS, DEFAULT_NAME, clamp } from './constants.js';
+export { paginate, formatName } from './helpers.js';