fix(agent): preserve upload Markdown provenance

[PeaceMaker-best]

Why

Web upload responses already identify the converted Markdown companion through markdown_file, including collision-renamed files such as a_1.md. That provenance was dropped before Agent execution, so UploadsMiddleware guessed <stem>.md. With same-stem uploads, the Agent could receive another document's outline; an explicit no-conversion result could also accidentally fall back to an unrelated Markdown file.

The explicit companion path was also validated separately from the later read. A writable sandbox process could replace the file between those operations and make unrelated content enter <current_uploads>.

What changed

• Preserve nullable markdown_file provenance in current-turn web-upload message metadata and use one shared frontend mapper for optimistic and submitted messages.
• Enforce tri-state Agent semantics: absent key keeps the legacy <stem>.md fallback, explicit null disables fallback, and a valid string selects only the named companion.
• Validate explicit basenames and fail closed for traversal, staging files, missing files, symlinks/reparse points, hard links, NTFS alternate data streams, and replacement races.
• Parse outline and preview from the same authoritative handle: directory-relative O_NOFOLLOW on POSIX and pinned, verified native handles on Windows.
• Keep raw companion metadata out of the model-visible <current_uploads> block and document the compatibility contract.

Surface area

• Frontend UI - page / component / setting / interaction under frontend/
• Backend API - endpoint / SSE event / request-response shape under backend/app
• Agents / LangGraph - Agent upload context and grounding behavior
• Sandbox - docker/ or sandboxed execution
• Skills - change under skills/
• Dependencies - no dependency changes
• Default behavior change - current-turn uploads now use explicit conversion provenance instead of guessing when the field is present
• Docs / tests / CI only - runtime behavior changes

Screenshots / Recording

Not applicable; this changes upload metadata propagation and Agent grounding, with no visual UI change.

Bug fix verification

• Reproduction tests: frontend/tests/unit/core/uploads/message-files.test.ts and backend/tests/test_uploads_middleware_core_logic.py.
• The provenance/crosstalk regressions went red before implementation (7 new backend failures plus the missing frontend mapper).
• The replacement-race, single-open preview, Windows directory-swap, and ADS regressions went red against the pre-fix implementation and green after the secure-handle change.

Validation

• Frontend: 989/989 tests passed across 126 files; ESLint, TypeScript, and Prettier checks passed.
• Backend changed area: 64 upload-middleware tests, 1 blocking-I/O anchor, and 32 file-outline compatibility tests passed.
• Ruff check/format, the repository blocking-I/O static detector, and git diff --check passed.
• Clean Windows full non-live comparison: this branch had 10,901 passed / 111 skipped / 132 failed; fresh origin/main had the exact same 132 failing node IDs (intersection 132, branch-only 0).

AI assistance

Tool(s) used: Codex

How you used it: Codex helped investigate the bug, draft the approved design, implement the change with RED/GREEN tests, run full validation, and perform independent task-level and final security reviews. This Draft PR intentionally leaves the human responsibility confirmation unchecked until the author personally reviews every line.

• I've read and understand every line of this change and take responsibility for it - it's not unreviewed AI output.

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