[atif-databraid]

Summary

A parent project's graph currently omits repositories mounted through directory symlinks, and Git-ignored reference repositories cannot be selected without changing ignore rules. Extend --follow-nested-repos to follow repository links, including linked worktrees, into one graph using their mounted paths and each child's Git ignore rules.

• Add repeatable, persisted --include-repo <path> to include selected repository mounts alongside normal project source, including mounts ignored by the parent. Retain the restricted --include-ignored-repos --only-dir form.
• Preserve saved directory restrictions across plain builds; add --all-dirs to clear them. Keep build, concept indexing, checks, and automatic refresh aligned.
• Preserve the independent submodule gate for explicitly selected gitlinks. Track physical repository targets during the existing walk and invalidate freshness when a mount changes targets, even if filenames, sizes, and timestamps match. Legacy fingerprints retain their filters and receive one identity-aware rebuild when nested repositories are enabled.
• Keep cycle detection based on active physical checkout paths while preserving logical mount paths for graph IDs. Broken links, file links, and links to ordinary directories remain excluded.

Validation

• 116 targeted tests passed across ingestion, nested repositories, submodules, directory/extension filtering, refresh, incremental builds, worktree seeding, and path normalization.
• Regression tests reproduced both the explicit-submodule bypass and stale refresh after symlink retargeting before the fixes; all pass afterward. Retarget coverage includes visible and explicitly included ignored mounts, plus legacy fingerprint migration and stable subsequent refreshes.
• tsc -p tsconfig.json --noEmit and git diff --check passed.

[trailhq-graft]

🌱 graft blast radius

5 areas changed → 5 areas can be affected. 18 dependent symbols, depth 2.
Tests: no test reaches Build Configuration, Context Discovery, File System Ingestion; 1 area updated its tests.
Tag: @anirudhkumar-nanonets — 10 of 10 areas · @shhdwi — 6 of 10 areas · @qoole — Context Discovery

flowchart TB
  A0(("Workspace Federation<br/>8 symbols"))
  A1(("Engine Orchestration<br/>4 symbols"))
  A2(("Pull Request Review<br/>4 symbols"))
  A3(("MCP Tool Integration<br/>1 symbol"))
  A4(("Check Context<br/>1 symbol"))
  classDef reached fill:#D9EDF3,stroke:#3AA7C9,stroke-width:1.5px,color:#0E313C;
  class A0,A1,A2,A3,A4 reached;

Loading

Can be affected	Symbols	Nearest hop	Reached from
Workspace Federation	8	src/graph/check.ts:L59-L159 checkGraph — calls, depth 1	Graph Construction, Build Configuration
Engine Orchestration	4	src/engine.ts:L104-L115 graph — calls, depth 1	Context Discovery, Graph Construction +1
Pull Request Review	4	src/app/review.ts:L45-L99 reviewPullRequest — calls, depth 1	Graph Construction, Build Configuration
MCP Tool Integration	1	src/mcp/tools.ts:L233-L262 callTool — calls, depth 2	Graph Construction
Check Context	1	src/context/check.ts:L39-L112 checkContext — calls, depth 1	Context Discovery, Build Configuration

Who knows this code — 4 people across 10 areas

Area	Who knows it
Graph Construction · changed	@anirudhkumar-nanonets — 19 commits, last 3mo ago · @shhdwi — 11 commits, last 14d ago
Build Configuration · changed	@anirudhkumar-nanonets — 13 commits, last 9d ago
Context Discovery · changed	@qoole — 4 commits, last 2d ago · @anirudhkumar-nanonets — 4 commits, last 3mo ago
CLI Entry Point · changed	@anirudhkumar-nanonets — 71 commits, last 3d ago · @shhdwi — 51 commits, last 14d ago
File System Ingestion · changed	@Frankie-Xu — 2 commits, last 2d ago · @anirudhkumar-nanonets — 3 commits, last 3mo ago
Workspace Federation · affected	@anirudhkumar-nanonets — 17 commits, last 9d ago · @shhdwi — 11 commits, last 14d ago
Engine Orchestration · affected	@anirudhkumar-nanonets — 17 commits, last 29d ago
Pull Request Review · affected	@anirudhkumar-nanonets — 11 commits, last 27d ago · @shhdwi — 2 commits, last 14d ago
…2 further areas

Ownership is git history over each area's own files, weighted towards recent work (120-day half-life). Merge commits and bots are dropped, and you are dropped from your own PR. A name with no @ has no GitHub handle in its commit email — tag them by hand, or add a .mailmap entry. A suggestion from history, not a CODEOWNERS rule.

All 18 dependent symbols, grouped by area

Workspace Federation — 8 symbols in 5 files

• src/graph/check.ts:L59-L159 — checkGraph (calls, depth 1)
  90: const sourceFiles = listSourceFiles(root, outDir, undefined, onlyDirs, committed.meta?.extensions);
• src/graph/refresh-run.ts:L18-L21 — main (calls, depth 1)
  20: await buildGraph(dir, { contextDir, graphOnly: true, onlyDirs, extensions });
• src/graph/refresh.ts:L202-L225 — rebuild (calls, depth 1)
  205: await buildGraph(args.dir, {
• src/graph/refresh.ts:L271-L347 — ensureFreshGraph (calls, depth 1)
  299: const drift = probeDrift(dir, outDir);
• src/graph/refresh-run.ts:L1-L33 — refresh-run.ts (calls, depth 2)
  9: import { buildGraph } from "./build.js";
• src/graph/refresh.ts:L355-L381 — ensureFreshChildren (calls, depth 2)
• src/graph/workspace-cli.ts:L65-L108 — buildChild (calls, depth 2)
  68: const childConfigPatch: BuildConfig = {};
• src/graph/workspace.ts:L631-L656 — federateCheck (calls, depth 2)
  652: for (const child of wg.missing) lines.push(`${child}/: not built (run ${cmd("graft build")})`);

Engine Orchestration — 4 symbols in 1 file

• src/engine.ts:L104-L115 — graph (calls, depth 1)
  105: return buildGraph(dir, {
• src/engine.ts:L72-L86 — init (calls, depth 2)
• src/engine.ts:L89-L91 — check (calls, depth 2)
• src/engine.ts:L95-L97 — checkGraph (calls, depth 2)

Pull Request Review — 4 symbols in 4 files

• src/app/review.ts:L45-L99 — reviewPullRequest (calls, depth 1)
  55: await buildGraph(checkout.dir);
• src/app/review-process.ts:L178-L182 — childReviewer (references, depth 2)
• src/app/review-worker.ts:L67-L87 — run (calls, depth 2)
• src/app/server.ts:L31-L37 — AppSeams (references, depth 2)

MCP Tool Integration — 1 symbol in 1 file

• src/mcp/tools.ts:L233-L262 — callTool (calls, depth 2)

Check Context — 1 symbol in 1 file

• src/context/check.ts:L39-L112 — checkContext (calls, depth 1)
  64: for (const file of listContextFiles(root, outDir, exts)) {

Test signal per changed area — 1 ✓ · 3 ✗ · 1 –

Reached = a node under a test path has a resolved edge into the changed symbol. It undercounts anything called indirectly — through a CLI, a spawned process or a dynamic import — so read a low ratio as “look here”, never as a coverage gate.

• ✓ Graph Construction — 3 of 5 reached · 4 test files changed here: test/context-only-dir.test.ts, test/graph-follow-nested-repos.test.ts, test/graph-only-dir.test.ts, test/ingest-fs.test.ts
  • not reached: writeFingerprint, listSourceFiles
• ✗ Build Configuration — 0 of 1 reached · no test file reaches it
  • not reached: readIncludeIgnoredRepos
• ✗ Context Discovery — 0 of 2 reached · no test file reaches it
  • not reached: resolveOnlyDirs, listContextFiles
• – CLI Entry Point — no function, method or class changed here
• ✗ File System Ingestion — 0 of 1 reached · no test file reaches it
  • not reached: gitVisibleFiles

57 test suites also reference this code

70 symbols, kept out of the diagram and the table so they cannot crowd out the areas a reviewer has to look at.

• test/ask-index.test.ts
• test/ask.test.ts
• test/claude-hooks.test.ts
• test/claude-prompt-private.test.ts
• test/container-extract.test.ts
• test/context-batch-stability.test.ts
• test/context-checkpoint.test.ts
• test/context-synth-cache-compat.test.ts
• test/context-synth-cache.test.ts
• test/context-synth-clamp.test.ts
• test/context-synth-concurrency.test.ts
• test/context.test.ts
• test/covers.test.ts
• test/depth-parity.ts
• test/generic-extract.test.ts
• test/graph-bash.test.ts
• test/graph-elixir.test.ts
• test/graph-extensions.test.ts
• test/graph-follow-submodules.test.ts
• test/graph-go.test.ts
• …37 more

⚠️ 2 changed files not in the graph (.trail/learnings/2026-11-11-explicit-repository-mounts-need-boundary-checks-atif.md, README.md) — no parser claims the extension, or the index predates the file.

_{graft blast · origin/main...HEAD · depth 2 · 14 changed files}

Open the interactive graph → — click an area to see its dependent symbols at file:line.