fix(opencode): bound apply patch diff metadata

[cyrilialab-prog]

fix(opencode): bound apply patch diff metadata

Closes #41733. Builds on and supersedes #41734.

Root cause

apply_patch persisted every file diff twice in tool metadata: once in
metadata.diff (combined) and once in metadata.files[].patch. For a delete,
the "diff" is the entire old file content, so deleting one large or binary file
(for example a 64 MiB archive or a .bin blob full of NUL bytes) wrote
hundreds of megabytes of binary text into:

• the permission request metadata,
• the completed tool part (part table),
• every durable message.part.updated.1 event emitted while the part streamed
  (event table).

In real sessions this grew opencode.db past 2.5 GiB, and the Desktop sidecar
died with exit code 5 while rehydrating the session, which surfaced in the UI
as TypeError: Failed to fetch in fetchMessages/loadMessages.

#41734 already stops the worst case for deletes by checking the extension,
file size, and a content sniff before reading. This PR keeps that behavior and
closes the remaining holes:

• Only deletes were protected. An add/update/move can still produce a
  pathological diff (for example a single-line file with no newlines, where
  diffLines treats the whole blob as one change).
• The combined metadata.diff was unbounded regardless of per-file limits, so
  a multi-file patch could still aggregate gigabytes.
• The omission marker did not say why content was omitted.

What this PR does

1. Commit 1 (from fix(opencode): omit unsafe delete diffs #41734): extract isBinaryFile into
   packages/opencode/src/util/binary.ts, and for deletes check extension,
   stat.size, and content NUL/printable ratio before reading; omit the
   content diff when binary or larger than 1 MiB.
2. Commit 2: add a final safety net for every change type. Each per-file diff
   is bounded to MAX_DIFF_BYTES (1 MiB) and the combined diff to
   MAX_TOTAL_DIFF_BYTES (2 MiB), with explicit markers:
   • binary file deleted (N bytes; content diff omitted)
   • oversized file deleted (N bytes; content diff omitted)
   • [diff truncated: showing first N of M bytes]

Truncation happens at line boundaries, so consumers never see a half-written
hunk; a single line larger than the cap is dropped entirely in favor of the
marker. The metadata always stays valid UTF-8 and JSON-encodable. The UI
degrades to a short marker instead of a crash; the actual file operation
result is unchanged.

Tests

packages/opencode/test/tool/apply_patch.test.ts, 35 passing:

• deletes a 64 MiB file without embedding its contents in metadata (marker
  contains the exact byte count, both result and permission metadata bounded,
  file removed)
• omits diffs for binary content without a binary extension (content sniffing,
  not just extensions)
• bounds metadata across a multi-file patch with mixed sizes (small file keeps
  its real diff, large file gets the marker, permission metadata equals result
  metadata)
• truncates the combined diff when per-file diffs exceed the aggregate cap
  (per-file diffs stay intact, combined diff capped at 2 MiB + marker)
• persists bounded apply_patch metadata and reloads it through the session
  store (Session.updatePart -> SQLite -> MessageV2.page; persisted tool
  state stays under 8 KiB)
• all pre-existing tests, including the fix(opencode): omit unsafe delete diffs #41734 binary/oversized delete cases
  and the PermissionV1 JSON-encodability check

Verification commands (from packages/opencode):

bun test test/tool/apply_patch.test.ts --timeout 60000
bun test test/tool/read.test.ts --timeout 60000
bun typecheck

Compatibility risks

• metadata.diff and metadata.files[].patch can now contain omission
  markers instead of full content. Consumers that parse these strings as
  unified diffs (UI diff renderers, external tooling reading tool metadata)
  will see a short Index:-style block or a truncated diff with an explicit
  marker. No schema change: both fields remain strings.
• deletions is 0 for omitted deletes (we intentionally do not read the
  file just to count lines). Consumers relying on exact deletion line counts
  for deleted oversized/binary files will see 0; the byte size is in the
  marker.
• Existing sessions written by older versions keep their oversized rows; the
  fix is write-side only and does not migrate data.

Migration plan for existing databases

The fix prevents new bloat. Databases already affected need a one-time
cleanup, run with the server stopped:

-- 1. Inspect oversized tool parts first
SELECT id, length(data) FROM part
WHERE type = 'tool' AND length(data) > 1000000
ORDER BY length(data) DESC;

-- 2a. Surgical: replace the combined diff only
-- (keeps the file list, diagnostics, and output)
UPDATE part
SET data = json_set(data, '$.state.metadata.diff',
  '[removed: oversized or binary delete diff]')
WHERE id IN (...);

-- 2b. Nuclear: parts still oversized after 2a carry bloat inside
-- state.metadata.files[].patch. Replace the whole metadata block
-- (loses the per-file list and diagnostics; keeps output).
-- Review the ids from step 1 first; narrow the WHERE to those ids
-- if any legitimate large-output parts show up.
UPDATE part
SET data = json_set(data, '$.state.metadata',
  json_object('diff', '[removed: oversized apply_patch metadata]'))
WHERE type = 'tool' AND length(data) > 1000000;

DELETE FROM event WHERE type = 'message.part.updated.1';
VACUUM;

Longer term, bounded event-log compaction would help every tool, not just
apply_patch (see #33356 and the closed #36710, closed only by automated
cleanup criteria, plus #40861/#42771 which address related summary-diff
payloads). Happy to split that into a separate PR if preferred.

[github-actions]

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[github-actions]

The following comment was made by an LLM, it may be inaccurate:

Based on my search, I found one related PR:

PR #41734: fix(opencode): omit unsafe delete diffs
#41734

Why it's related: The current PR (46656) explicitly mentions that it "Builds on and supersedes #41734." This is not a duplicate—rather, PR #41734 is a predecessor that handles the initial part of the fix (protecting deletes by checking extension, file size, and content sniff), while PR #46656 extends this with comprehensive bounds for all change types and explicit truncation markers.

No actual duplicate PRs found.

[github-actions]

This pull request has been automatically closed because it was not updated to meet our contributing guidelines within the 2-hour window.

Feel free to open a new pull request that follows our guidelines.

[rnwst]

@cyrilialab-prog - would you mind re-submitting this PR, this time using the correct PR template? I just had several crashes due to this issue, and it would be great to see this fixed! Seeing as you have already done the work, using the appropriate template would seem like a small hurdle to overcome :)