fix(filesystem): enforce containment and race-safe repository file operations — symlinks and path races can redirect writes or exports

[unohee]

Summary

Published because this run stopped and needs a human: autonomous execution failed 4 times

It has not been reviewed and is very likely incomplete — this PR is a draft on purpose. It exists so the work is reviewable instead of sitting on a branch that was never pushed.

Change shape

529 file(s): 257 source · 233 test · 7 docs · 32 other

Base freshness

Branch base is 244 commit(s) behind main at publication.

⚠ Conflicts with main in: src/cli/designPipeline.ts, src/knowledge/gitInfo.ts
GitHub runs no pull_request workflows on a PR it cannot merge, so any green checks here are not the verification gate. Opened as a draft; rebase before review.

⚠️ File overlap with in-flight work

This branch changes files that other open PRs / active branches also touch. Coordinate before merging to avoid divergent parallel edits (INT-2388 #3):

• PR fix(repository): harden filesystem, Git, and verification boundaries — prevent race conditions, ambiguous rollback, and unsafe execution #759 (swarm/AGT-3447-fix-repository-harden-filesystem-git-and) — 3 file(s): src/knowledge/gitInfo.ts, src/knowledge/graphqlExporter.ts, src/tui/inputDebug.ts
• ⚠️ MERGED PR feat(adapters): Ollama Cloud adapter with per-transport model ids (AGT-4512) #720 (feat/ollama-cloud-adapter) — not in this branch's history, verify its fix wasn't dropped — 1 file(s): src/cli/initWizard.ts
• ⚠️ MERGED PR fix(agent-execution): quarantine malformed bus history and fail fan-out baseline loudly (AGT-3487) #718 (heewonoh/agt-3487-artifact-failsafe) — not in this branch's history, verify its fix wasn't dropped — 1 file(s): src/knowledge/gitInfo.ts
• ⚠️ MERGED PR fix(knowledge-registry): surface incomplete scans and untracked discovery (AGT-3490) #717 (heewonoh/agt-3490-coverage-signal) — not in this branch's history, verify its fix wasn't dropped — 1 file(s): src/knowledge/gitInfo.ts

Linear

Closes AGT-3431

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🤖 Generated with OpenSwarm

[unohee]

Closing: triaged DROP — API-incompatible rewrite that cannot compile (graphqlExporter.ts calls graph.getNodes/getEdges and drops KnowledgeGraph fields other files import); only ~25-line residue duplicates #759. Not mergeable in this form; nothing unique worth preserving beyond what main already has.