The server broadcasts otUpdateApplied (with ops) to ALL clients including
the sender. Our bridge was treating its own echoed ops as remote ops and
re-applying them, causing text duplication (e.g. "simulatorimulator").

Rewrite OT handling to match Overleaf's ShareJS _onMessage pattern:
- ACK = no ops OR meta.source matches our publicId (own echo)
- REMOTE = ops from a different source
- ACK path calls onAck() without re-applying ops
- OtClient silently drops duplicate acks in synchronized state
- OtClient drops stale remote ops (version < current)
- Remove pendingEchos counter in favor of meta.source detection

Also: refresh MCP comment contexts on new-comment/delete-thread events,
add Overleaf reference repo to .gitignore.

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

When addEditorDoc is called while the bridge has in-flight OT ops
(awaitingConfirm), the ack/error response was ignored because
handleOtUpdate/handleOtError skipped editor docs entirely. This left
the bridge's OtClient stuck and the edit appeared lost until
removeEditorDoc re-discovered the discrepancy.

Fix: always process acks regardless of editor doc status, and only
skip OT errors for editor docs when the bridge has no OtClient.

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

- Online users: click "N online" badge to see user names with cursor colors
- MCP get_online_users tool: main process tracks users in .lattex-online-users.json
- CLAUDE.md: show current user's Overleaf name (fetched from /user/settings)
- CLAUDE.md: mandatory first steps with MUST/NEVER language at top of file
- claude-workspace/ directory: untracked scratch space for Claude Code experiments
- chokidar + bridge skip claude-workspace/ to prevent syncing to Overleaf

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

- Fix .bib (and other non-active tab) edits disappearing: call otLeaveDoc
  on tab switch so bridge takes back OT ownership; release .bib pre-loads
  immediately after reading content for citation autocomplete
- Always update lastKnownContent in processDocChange for editor docs to
  prevent stale state accumulation
- Flush pending OT ops in OverleafDocSync.destroy() before tab switch
- Add three-way merge in replaceContent to preserve concurrent remote edits
- Wire MCP compile to UI: file-based signal between MCP server and Electron
  main process, with compile animation and PDF refresh in renderer
- Add CLSI flush before compile to prevent stale cached results
- Add OT error recovery: re-join doc and re-apply disk changes on otUpdateError
- Add bridge reconnect handling: reset OtClient on docRejoined for non-editor docs
- Add compile concurrency lock to prevent duplicate compiles
- removeEditorDoc compares disk vs server content to catch in-flight ops

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

When Claude Code writes to disk, a debounce timer is set. If a remote
Overleaf op arrives during the debounce, onEditorContentChanged would
write the remote content back to disk, overwriting Claude Code's edit.

Fix: skip disk write and lastKnownContent update in onEditorContentChanged
when a debounce is pending (external disk change waiting to be processed).
Also increase writesInProgress guard to 800ms to exceed chokidar's 500ms
polling interval.

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

- Exclude CLAUDE.md from sync (move to .claude/ dotfile dir, clean up root copy)
- Add Ctrl+wheel font zoom for editor (capture phase, disable Electron built-in zoom)
- Load cached PDF on project connect (avoid recompile to see last PDF)
- Add synctex debug logging for PDF↔source navigation troubleshooting
- Fix .claude/ dir creation order (mkdir before write)

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

The root cause of server compile failures was that output.pdf was being
saved into the synced project directory, causing FileSyncBridge to upload
it back to Overleaf as a project file. CLSI then failed because it found
an existing output.pdf blocking its compilation output.

Changes:
- Save compile artifacts (PDF, synctex.gz) to .build/ subdirectory instead
  of the synced project root — .build is a dotfile dir ignored by chokidar
- Add pdf/pdfxref/stderr/stdout/chktex to FileSyncBridge ignore patterns
- Add rootResourcePath to compile request body (matches Overleaf web client)
- Implement PDF download with fallback via direct build ID URL construction
- Add server compile handler, compile dropdown menu, PDF save button
- Fix resolved comment highlight flash on startup (null initial state)
- Fix EPIPE crash on startup when stdout/stderr is closed
- Fix synctex inverse search to use relative paths via OT doc join

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

- Sync new local files (created by Claude Code etc.) to Overleaf via REST API
- Create intermediate folders as needed, handle both text docs and binaries
- Scan for orphaned files on startup that weren't synced previously
- Add "Copy Comments" quick action: copies unresolved comments for current file
  to clipboard with line numbers, context, author names, and timestamps
- Filter comments to active file only, exclude resolved threads

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

Root cause: SHA-1 hash sent with applyOtUpdate didn't match Overleaf's
server-side computation, causing "Invalid hash" error, disconnect, and
rollback of all synced changes.

- Remove hash field from applyOtUpdate to skip server-side hash check
- Switch applyOtUpdate from fire-and-forget to emitWithAck for reliable ack
- Fix getOldDoc bug: save base doc when changes start accumulating instead
  of incorrectly using current doc (caused wrong delete ops)
- Fix ack handler: only ack when no 'op' field (was acking remote ops too)
- Await fileSyncBridge.start() instead of fire-and-forget
- Add joinDoc retry logic for transient joinLeaveEpoch mismatch errors
- Clear pending ack callbacks on WebSocket close to prevent timeout errors
- Add otUpdateError logging for server-side rejections
- Add file-based bridge logging for debugging sync issues

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>