Fix workspace switch race condition, gh auth detection, and file open perf

[RajPabnani03]

Summary

Fixes three open bugs (#581, #551, #572) and adds project MCP servers and skills for streamlined development.

---

Bug Fixes

1. Bug #581 — Workspace State Not Preserved When Switching Folders

Root Cause: In switchToProject(), the old project's buffers were closed after the new project's background initialization (including session restore) was kicked off via void (async () => { ... })(). This created a race condition where closing old terminal buffers could kill PTY processes that the new project's restored terminals were trying to use, or vice versa.

Fix: Move closeBuffersBatch() to execute before the new project's directory reading and session restore, ensuring old workspace state is cleanly torn down before new state is loaded.

2. Bug #551 — Athas not detecting that GitHub CLI is authenticated

Root Cause: gh auth status can return exit code 0 even when the token is expired or invalid (known upstream issue cli/cli#8845). The original code only checked output.status.success(), so it would report "authenticated" for invalid/expired tokens.

Fix: Parse stderr output to check for authentication failure indicators ("not logged in", "token is invalid", "Failed to log in", etc.) even when exit code is 0. Also check for "Logged in to" as positive confirmation when exit code is 0.

3. Bug #572 — Athas Lags on CachyOS / File Opening Performance

Root Causes:

1. readDirectoryContents() called getSymlinkInfo() (a stat syscall via Tauri IPC) for every single entry in a directory. For large projects with hundreds/thousands of files, this meant hundreds of sequential I/O calls just to list a directory.
2. handleFileSelect() read files twice — once for binary sniffing (readFile) and once for content (readFileContent), doubling I/O for every file open.

Fixes:

1. Remove per-entry symlink resolution from readDirectoryContents(). Symlinks are still resolved lazily when a file is opened (in handleFileSelect) or when a directory is expanded. This eliminates hundreds of stat syscalls during directory listing.
2. Combine binary sniffing and content reading into a single readFile() call. The raw bytes are read once, checked for binary content, and then decoded to UTF-8 text using TextDecoder instead of reading the file a second time.

Changed Files

File	Change
crates/github/src/api.rs	Parse gh auth status stderr for auth state instead of relying on exit code alone
src/features/file-system/controllers/file-operations.ts	Remove per-entry symlink resolution from readDirectoryContents()
src/features/file-system/controllers/store.ts	Move closeBuffersBatch() before project switch; combine binary sniff + content read into single I/O pass

Testing

• TypeScript type-check passes (tsc --noEmit)
• oxlint passes on changed files
• rustfmt passes on crates/github/src/api.rs

---

MCP Servers & Skills

MCP Servers (.factory/mcp.json)

Server	Type	Purpose
GitHub	HTTP	Full GitHub API access — repos, issues, PRs, code search, actions
Sequential Thinking	Stdio	Structured step-by-step reasoning for debugging and planning
Playwright	Stdio	Browser testing and automation
Sentry	HTTP	Error tracking and performance monitoring
Linear	HTTP	Issue tracking and project management

Skills (.factory/skills/)

Skill	Purpose	Invocation
athas-bug-fix	Standardized bug diagnosis and fix workflow	Auto (mentions "bug", "fix", "issue")
athas-performance	Performance bottleneck identification and optimization	Auto (mentions "lag", "slow", "performance")
athas-release	Release process following project conventions	Manual only (/athas-release)
athas-contribution	Contribution standards and commit conventions	Auto (mentions "contribute", "PR", "commit")