fix(mcp): preserve TOML multiline strings during removal

[Frankie-Xu]

Removing or rewriting a Graft TOML entry can mistake [mcp_servers.graft.env] inside another server's multiline string for an owned table. It then deletes the string's closing delimiter and following foreign settings, leaving invalid TOML. The removal scanner now tracks basic/literal string context, including comments, escapes and four/five-quote endings, and preserves foreign string content and newline delimiters.

This is a focused follow-up to #547. That PR is currently unmerged, so this branch retains its canonical parent/subtable cleanup commits; the additional commit e36ba64b8bdb7daa49fc7bd897fdcb770dc0a42c handles multiline-string preservation. It preserves orphan and noncontiguous canonical Graft-subtable cleanup and adds no runtime dependency or TOML reserialization.

A separate CI-only commit reuses the shared fix from e9649a4cda39f9bae7264e4f6d642e466dd46d0c to align CodeQL init with the existing analyze pin at v4.38.1. It changes one workflow line; functional source remains the independently reviewed commit above.

Validation:

• The 11 new unit/writer regressions fail on the exact fix(mcp): remove graft TOML subtables on uninstall #547 head; all 26 pass with this change.
• All 28 retract tests pass, including synthetic Codex config removal and the subsequent no-op.
• An independent Python tomllib oracle passes 19 fixtures with valid output and preserved foreign values. Independent review adds 168 valid string-boundary probes, all passing.
• npm run build passes locally. On exact published head 9e8878a, official clean-install prepare/build and full Ubuntu/Windows CI pass: 1,376 / 1,371 passed; 1 / 6 expected skips; zero failures. Node 24 WASM and CodeQL pass. The still-unstarted duplicate local host suite was canceled after these official substitutes passed.
• git diff --check passes; independent code/spec review found no actionable issues.

Existing noncanonical-header/array-table matching and nested-array boundary limitations are outside this string-focused follow-up. The nested-array behavior was reproduced on upstream main and #547 as well as this branch. New Codex registration/retract fixtures use temporary synthetic homes; existing repo-only retraction fixtures disable global writes. Native dependency compilation encountered a local missing C++ header; the affected tests ran using an exact-version, verified read-only N-API cache copied into this isolated checkout.

AI-assisted implementation and review.

[github-actions]

🌱 graft blast radius

1 area changed → 1 area can be affected. 1 dependent symbol, depth 2.
Tests: no test reaches MCP Configuration.
Tag: @anirudhkumar-nanonets — MCP Configuration, Configuration Retraction · @shhdwi — MCP Configuration, Configuration Retraction

flowchart TB
  A0(("Configuration Retraction<br/>1 symbol"))
  classDef reached fill:#D9EDF3,stroke:#3AA7C9,stroke-width:1.5px,color:#0E313C;
  class A0 reached;

Loading

Can be affected	Symbols	Nearest hop	Reached from
Configuration Retraction	1	src/hosts/retract.ts:L211-L221 removeTomlSection — calls, depth 2	MCP Configuration

Who knows this code — 2 people across 2 areas

Area	Who knows it
MCP Configuration · changed	@anirudhkumar-nanonets — 5 commits, last 2d ago · @shhdwi — 4 commits, last yesterday
Configuration Retraction · affected	@anirudhkumar-nanonets — 5 commits, last today · @shhdwi — 1 commit, last yesterday

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 1 dependent symbol, grouped by area

Configuration Retraction — 1 symbol in 1 file

• src/hosts/retract.ts:L211-L221 — removeTomlSection (calls, depth 2)

Test signal per changed area — 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.

• ✗ MCP Configuration — 0 of 2 reached · no test file reaches it
  • not reached: nextTomlMultilineQuote, isFamilyHeader

_{graft blast · origin/main...HEAD · depth 2 · 3 changed files}

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