fix(deep): coerce stringified concept-pass nodes and stop ticking empty batches (#383)

[Frankie-Xu]

Summary

• A forced record_graph call can still deliver nodes as a JSON string (double-encoded tool args). clean() then hit if (!Array.isArray(nodes)) return [], warnToolChoiceIgnored stayed silent because there was a tool call, and the CLI printed ✓ concepts: 0 nodes for a complete graph (--deep concept pass: a stringified nodes tool argument is dropped by clean(), and the empty batch prints a ✓ #383).
• Coerce a string nodes with JSON.parse; if a stray brace breaks that, salvage balanced {name:…} objects. Warn with the received type, character count, tool-call count, and how many nodes were salvaged.
• A genuine empty array still yields 0 nodes, but that batch is a ⚠ rather than a success tick.

Not in this PR

• Does not raise maxTokens.
• Does not change crux.ts / id peel.
• Does not reuse recoverToolArgsFromContent (that path only runs when there is no tool-call args object).

Closes #383

Test plan

• 12k stringified nodes with a stray } between two objects → salvaged nodes + warning
• Empty nodes array → 0 nodes, warning, no ✓
• node --import tsx --test test/synthesize-clean.test.ts test/llm-ops.test.ts

Made with Cursor

[github-actions]

🌱 graft blast radius

Nothing outside this diff depends on it. 2 areas changed; no indexed dependents at depth 2.
Tests: no test reaches Graph Synthesis.
Tag: @anirudhkumar-nanonets — Graph Synthesis, CLI · @shhdwi — Graph Synthesis, CLI

Who knows this code — 2 people across 2 areas

Area	Who knows it
Graph Synthesis · changed	@anirudhkumar-nanonets — 4 commits, last 2mo ago · @shhdwi — 1 commit, last 2mo ago
CLI · changed	@anirudhkumar-nanonets — 39 commits, last 5d ago · @shhdwi — 23 commits, last 1mo 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.

Test signal per changed area — 1 ✗ · 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 Synthesis — 0 of 5 reached · no test file reaches it
  • not reached: balancedClose, coerceRecordGraphNodes, salvageNamedObjects, shapeOfNodes, synthesize
• – CLI — no function, method or class changed here

_{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.

[Frankie-Xu]

Follow-up: the previous commit stored these files as CRLF on Windows, so GitHub showed a whole-file rewrite of cli.ts. e780182 converts them back to LF to match main. Behaviour is unchanged; the real delta is synthesize.ts + the concept-pass tick in cli.ts + test/synthesize-clean.test.ts.