Egonex-AI/Understand-Anything · error

Assembled graph is missing whole-file nodes for analyzed pat

Error message

Assembled graph is missing whole-file nodes for analyzed paths: ${missingAnalyzedPaths.join(', ')}; baseline not advanced

What it means

After assembling the updated graph, finalize verifies that every path in plan.filesToReanalyze has whole-file node coverage in the assembled output (via hasAnalyzedFileCoverage). If any reanalyzed file produced no corresponding whole-file node, the graph would silently lose coverage for that file, so the script throws and leaves the baseline unadvanced. This is an anti-data-loss invariant for incremental updates.

Source

Thrown at understand-anything-plugin/skills/understand/finalize-incremental.mjs:441

  if (plan.action !== 'SKIP') {
    const previousGraph = readJson(graphPath, {});
    const assembledRaw = readJson(join(intermediateDir, 'assembled-graph.json'));
    if (!assembledRaw || !Array.isArray(assembledRaw.nodes) || !Array.isArray(assembledRaw.edges)) {
      throw new Error('assembled-graph.json is missing or invalid; baseline not advanced');
    }
    const assembled = refreshGraphImports(
      normalizeAssembled(assembledRaw),
      scan.importMap ?? {},
      importMapRefreshPaths,
    );
    const nodeIds = new Set(assembled.nodes.map(node => node.id));
    const pathIndex = buildPathIndex(assembled.nodes);
    const missingAnalyzedPaths = plan.filesToReanalyze.filter(
      path => !hasAnalyzedFileCoverage(assembled.nodes, path),
    );
    if (missingAnalyzedPaths.length > 0) {
      throw new Error(
        `Assembled graph is missing whole-file nodes for analyzed paths: ` +
        `${missingAnalyzedPaths.join(', ')}; baseline not advanced`,
      );
    }
    if (plan.rerunArchitecture && !existsSync(join(intermediateDir, 'layers.json'))) {
      throw new Error('Architecture update requires layers.json; baseline not advanced');
    }
    if (plan.rerunTour && !existsSync(join(intermediateDir, 'tour.json'))) {
      throw new Error('Architecture update requires tour.json; baseline not advanced');
    }
    const rawLayers = plan.rerunArchitecture
      ? readJson(join(intermediateDir, 'layers.json'))
      : previousGraph.layers ?? [];
    const rawTour = plan.rerunTour
      ? readJson(join(intermediateDir, 'tour.json'))
      : previousGraph.tour ?? [];
    const now = new Date().toISOString();
    const graph = {

View on GitHub (pinned to 07edf82a04)

Solutions

1. Regenerate the incremental plan so filesToReanalyze matches files that actually exist, then rerun analysis and finalize
2. Check the listed missing paths: if files were deleted/renamed, replan instead of reusing the stale plan
3. Inspect the analyzer logs for the listed paths to find parse failures, then fix or exclude those files
4. Ensure path normalization (forward slashes, relative to project root) matches between plan, scan, and assembler

Example fix

// before: plan references a deleted file
"filesToReanalyze": ["src/old-name.ts"]  // file no longer exists
// Error: Assembled graph is missing whole-file nodes for analyzed paths: src/old-name.ts ...

// after: replan so deleted files are excluded
rm .ua/intermediate/incremental-plan.json && rerun /understand incremental
// plan.filesToReanalyze now reflects the current tree

const plan = JSON.parse(fs.readFileSync('.ua/intermediate/incremental-plan.json','utf8'));
const missing = plan.filesToReanalyze.filter(p => !fs.existsSync(path.join(projectRoot, p)));
if (missing.length) throw new Error(`Stale plan paths (deleted/renamed): ${missing.join(', ')}; replan first`);

const hasFullCoverage = (assembled, plan) =>
  plan.filesToReanalyze.every(p => assembled.nodes.some(n => n.path === p && n.type === 'file'));

try {
  await run('node finalize-incremental.mjs .');
} catch (err) {
  if (String(err.message).includes('missing whole-file nodes for analyzed paths')) {
    fs.rmSync('.ua/intermediate/incremental-plan.json', { force: true });
    await replanAndRerunIncremental();
  } else throw err;
}

When it happens

Trigger: An analysis agent returned an empty or partial result for one of plan.filesToReanalyze; a renamed/deleted file is still listed in filesToReanalyze; the assembler dropped nodes for files whose parsing failed; path casing/normalization mismatches make hasAnalyzedFileCoverage miss the node.

Common situations: File deleted from the working tree after planning but before analysis; syntax-error or unsupported-language file the analyzer skips; Windows/POSIX path separator differences; merge that both renamed and modified files, so the plan references the old path.

Understand the failure class

Background: "This is a bug, please report it": internal invariant violations, unreachable panics, and SNH errors explained — this error's family across 47 libraries.

Related errors

• knowledge-graph.json is missing or invalid; baseline not adv
• assembled-graph.json is missing or invalid; baseline not adv
• Invalid knowledge graph: ${result.fatal ?? "unknown error"}
• Invalid domain graph: ${result.fatal ?? "unknown error"}
• Freshness response was malformed

AI-assisted analysis of Egonex-AI/Understand-Anything@07edf82a04 (2026-09-07). Data as JSON: /api/errors/b783bbc22d4b169c. Report an issue: GitHub.