Flatten Git service layer and switch server paths to base dir

[juliusmarminge]

Summary

• Flattened the git service abstraction into GitCore, removing the separate GitService layer and updating downstream consumers and tests.
• Introduced base-directory driven path derivation so state, logs, worktrees, and attachments are resolved from T3CODE_HOME / --base-dir.
• Updated desktop and server bootstrapping, docs, and integration tests to use the new derived path layout.
• Adjusted attachment resolution to work from an explicit attachments directory instead of the full state directory.

Testing

• Not run (PR content only).
• Existing test coverage was updated across git, orchestration, attachment, and server config layers.
• Project checks expected before merge: bun fmt, bun lint, bun typecheck, and bun run test.

Note

Replace GitService with GitCore as the primary git execution layer

• Removes GitService from the runtime and test layers, making GitCore the single service responsible for executing git commands.
• Adds an execute method to GitCoreShape that spawns a git child process with streamed stdout/stderr, a 30s default timeout, and a 1,000,000-byte per-stream output cap.
• Non-zero exit codes raise GitCommandError unless explicitly permitted; timeouts and stream failures are also wrapped as GitCommandError with operation, command, and cwd context.
• CheckpointStoreLive no longer implicitly provides GitService; callers must now supply GitCore explicitly.
• Risk: all git operations now enforce a 1MB output limit and a 30s timeout by default, which may cause GitCommandError for commands that previously succeeded with large output or slow execution.

^{Macroscope summarized 5156493.}

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✨ Finishing Touches

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