chore(server): port upstream server quick wins (2026-10-09)

[TheDarkPhantom]

The fork has not merged upstream since 2026-07-30, so a batch of small upstream server fixes was missing. This hand-ports the ones that apply to the fork's V1 server, one commit each, with upstream tests adapted.

Ported

• fix(server): preserve staging during commit message generation pingdotgg/t3code#15532 preserve staging during commit message generation: the diff is built in a temporary GIT_INDEX_FILE, so the user's staged selection, split-index files and merge metadata are untouched; staging moves to commit time. Adapted to the fork's runGit signature via a small runGitWithOptions helper.
• fix(server): probe project favicon candidates concurrently pingdotgg/t3code#12543 probe project favicon candidates concurrently (first hit in list order wins).
• fix(observability): a failing trace disk no longer stalls the server pingdotgg/t3code#13758 a failing trace disk no longer stalls the server: failed trace batches are dropped instead of re-queued, with one log on failure and one on recovery.
• fix(server): return partial workspace index on timeout pingdotgg/t3code#11500 return partial workspace index on timeout: a slow first scan serves what it has (truncated) instead of failing. The fork has one paths-only index, so the upstream variant check is dropped.
• fix(server): name the cause of a failed git command pingdotgg/t3code#8645 name the cause of a failed git command: GitCommandError gains an optional closed reason tag classified from git's diagnostic lines (stderr still never leaves the driver).
• perf(shared): scan PATH once per command before spawning, not on every spawn pingdotgg/t3code#12600 scan PATH once per command before spawning: successful Windows spawn lookups are cached for 30s. The fork lacks upstream's shared command-resolution cache, so this adds a dedicated SpawnResolutionCache.
• fix(server): one failing RPC handler no longer ends the client's other requests pingdotgg/t3code#15515 one failing RPC handler no longer ends the client's other requests: WebSocket RPC runs with disableFatalDefects plus a small DefectReporter; effect-acp isolates notification handlers, answers dying request handlers, and terminates on a reader-callback defect.
• fix(server): end clone options before the repository URL pingdotgg/t3code#14781 end clone options before the repository URL (git clone -- <url> <dir>).

Skipped

• fix(server): idle shells stop reloading every project once a minute pingdotgg/t3code#14893 (idle shells reload every project once a minute): the loop lives in the orchestration-v2 shell enrichment stream, which the fork does not have.
• fix(server): project favicons stop being rescanned every minute pingdotgg/t3code#16206 (favicons rescanned every minute): changes ProjectEnrichmentService, which the fork does not have; fork favicons are resolved per asset request.
• fix(server): honor submodule settings when creating worktrees pingdotgg/t3code#15594 (submodule settings for worktrees): the fork has no worktreeSubmodules setting.
• fix(server): editors appear once a slow discovery scan finishes pingdotgg/t3code#13917 (editors appear after a slow discovery scan): the fork already moved editor discovery off the config path into a background EditorDiscovery service that pushes availableEditorsUpdated.
• fix(server): expand home-relative media paths pingdotgg/t3code#15618 (home-relative media paths): the fork has no media-file asset resource.

Verification

• vp test run on every touched test file: 243 passed, 5 failed. All 5 also fail on the unmodified code and are Windows-only path issues (backslash vs / assertions in ProjectFaviconResolver and SourceControlRepositoryService, newline worktree path in GitVcsDriverCore).
• Each new upstream test was confirmed to fail without its fix.
• tsgo --noEmit clean for apps/server, packages/shared, packages/effect-acp, packages/contracts.
• vp lint and vp fmt --check clean on changed files; vp run check:avicode and vp run test:avicode pass.

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