fix(deep): honor --only-dir in the concept pass (#252)

[Frankie-Xu]

Summary

• graft build --deep now applies the same --only-dir whitelist as the wiring walk (filterByOnlyDirs), so the concept pass no longer summarizes or synthesizes files outside the prefixes.
• checkContext reads the same file set (CLI/API, else the fingerprint, matching checkGraph / probeDrift) so graft check does not report excluded files as coverage.
• Wiring behavior is unchanged; --only-dir prefix / repeatable semantics are the same as feat: add --only-dir whitelist to graft build #149.

Closes #252

Test plan

• node --import tsx --test test/context-only-dir.test.ts — concept summaries, multi --only-dir, fingerprint fallback, checkContext, Graft.init, wiring still scoped
• node --import tsx --test test/graph-only-dir.test.ts — existing whitelist + fingerprint probe still clean
• npm test — full suite (1065 passing locally)

Made with Cursor

[trailhq-graft]

🌱 graft blast radius

2 areas changed → 2 areas can be affected. 3 dependent symbols, depth 2.
Tests: 2 areas updated their tests.
Tag: @anirudhkumar-nanonets — 4 of 4 areas · @shhdwi — 4 of 4 areas

flowchart TB
  A0(("Workspace Splitting<br/>2 symbols"))
  A1(("MCP Tool Invocation<br/>1 symbol"))
  classDef reached fill:#D9EDF3,stroke:#3AA7C9,stroke-width:1.5px,color:#0E313C;
  class A0,A1 reached;

Loading

Can be affected	Symbols	Nearest hop	Reached from
Workspace Splitting	2	src/graph/workspace-cli.ts:L49-L70 buildChild — calls, depth 1	Context Building, CLI Initialization
MCP Tool Invocation	1	src/mcp/tools.ts:L256-L338 callSingleTool — calls, depth 2	Context Building

Who knows this code — 2 people across 4 areas

Area	Who knows it
Context Building · changed	@anirudhkumar-nanonets — 5 commits, last 9d ago · @shhdwi — 3 commits, last 11d ago
CLI Initialization · changed	@anirudhkumar-nanonets — 36 commits, last 2d ago · @shhdwi — 24 commits, last 16d ago
Workspace Splitting · affected	@shhdwi — 6 commits, last 17d ago · @anirudhkumar-nanonets — 3 commits, last 18d ago
MCP Tool Invocation · affected	@shhdwi — 14 commits, last 17d ago · @anirudhkumar-nanonets — 6 commits, last 18d ago

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 3 dependent symbols, grouped by area

Workspace Splitting — 2 symbols in 2 files

• src/graph/workspace-cli.ts:L49-L70 — buildChild (calls, depth 1)
  66: if (opts.deep) await engine.init(childDir, { extensions: opts.extensions });
• src/graph/workspace.ts:L493-L506 — splitWorkspace (calls, depth 2)

MCP Tool Invocation — 1 symbol in 1 file

• src/mcp/tools.ts:L256-L338 — callSingleTool (calls, depth 2)

Test signal per changed area — 2 ✓

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.

• ✓ Context Building — 2 of 4 reached · 1 test file changed here: test/context-only-dir.test.ts
  • not reached: listContextFiles, resolveOnlyDirs
• ✓ CLI Initialization — 1 of 1 reached · 1 test file changed here: test/context-only-dir.test.ts

4 test suites also reference this code

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

• test/context-checkpoint.test.ts
• test/context.test.ts
• test/covers.test.ts
• test/utf16-source.test.ts

_{graft blast · origin/main...HEAD · depth 2 · 5 changed files}

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

[shhdwi]

Verified locally on top of current main (clean merge incl. #254; build clean).

Reproduced #252 with an offline recording summarizer: graft build --deep --only-dir src on base main summarized the WHOLE repo (docs/c.ts, src/a.ts, tools/b.ts) — out-of-scope work + full re-synthesis. With this PR only src/a.ts is summarized/synthesized. Nice that listContextFiles/filterByOnlyDirs reads the CLI value else the graph fingerprint (mirroring probeDrift) and is shared by checkContext, so build and check can't disagree. context-only-dir 6/6, graph-only-dir 2/2, context+check 30/30. Fixes #252. Merging.