refactor(effect): use Git service in file and storage

[kitlangton]

Summary

• replace remaining internal Git.run(...) facade hops in FileWatcher, Storage migrations, and File with direct Git.Service usage
• keep the new git requirements at the correct composition boundary by updating the affected default layers and manual test layers
• simplify File's internal git usage with a small local gitText helper and by reusing git.show(...) for original file content

Notes

• file/index.ts was the trickiest file in this sweep because its old Effect.promise(async () => ...) blocks mixed git subprocess calls with non-git file-content work. The fix was to pull only the git subprocess pieces into Git.Service while leaving the rest of the file-content logic unchanged.
• I reviewed the diff for simplification after the first pass. I kept the worthwhile local cleanups, but did not broaden this PR into larger reuse changes like switching storage migration identity logic over to Project or changing file status behavior more aggressively.

Testing

• bun typecheck
• bun turbo typecheck
• bun run test -- test/storage/storage.test.ts test/file/watcher.test.ts