[Bug] Tracked files lost local changes after `git checkout -- .` and untracked files deleted after `git clean -fd`

Bug Description
משת הקבצים ה־tracked איבדו את השינויים המקומיים שלהם בגלל git checkout -- .
stage_visual_diagnostics.py ושאר קבצי הלוגים ה־untracked נמחקו בגלל git clean -fd

Environment Info

• Platform: win32
• Terminal: windows-terminal
• Version: 2.1.101
• Feedback ID: 7d7fb44b-502d-4d5b-8fe5-010c4764bade

Errors

[{"error":"Error: ENOENT: no such file or directory, unlink 'C:\\Users\\yossi\\AppData\\Local\\Temp\\claude\\C--Users-yossi-PycharmProjects-PythonProject2\\8b06513c-bb53-42c0-89b7-4f6985686345\\tasks\\a0701036a2bbd6c95.output'\n    at async <anonymous> (B:/~BUN/root/src/entrypoints/cli.js:7823:299)","timestamp":"2026-04-12T09:21:58.798Z"},{"error":"MaxFileReadTokenExceededError: File content (13194 tokens) exceeds maximum allowed tokens (10000). Use offset and limit parameters to read specific portions of the file, or search for specific content instead of reading the whole file.\n    at KO_ (B:/~BUN/root/src/entrypoints/cli.js:4500:12874)\n    at processTicksAndRejections (native:7:39)","timestamp":"2026-04-12T09:22:01.034Z"},{"error":"Error: ENOENT: no such file or directory, unlink 'C:\\Users\\yossi\\AppData\\Local\\Temp\\claude\\C--Users-yossi-PycharmProjects-PythonProject2\\8b06513c-bb53-42c0-89b7-4f6985686345\\tasks\\aa2016c19b09672af.output'\n    at async <anonymous> (B:/~BUN/root/src/entrypoints/cli.js:7823:299)","timestamp":"2026-04-12T09:22:06.872Z"},{"error":"MaxFileReadTokenExceededError: File content (15896 tokens) exceeds maximum allowed tokens (10000). Use offset and limit parameters to read specific portions of the file, or search for specific content instead of reading the whole file.\n    at KO_ (B:/~BUN/root/src/entrypoints/cli.js:4500:12874)\n    at processTicksAndRejections (native:7:39)","timestamp":"2026-04-12T09:22:08.910Z"},{"error":"MaxFileReadTokenExceededError: File content (17411 tokens) exceeds maximum allowed tokens (10000). Use offset and limit parameters to read specific portions of the file, or search for specific content instead of reading the whole file.\n    at KO_ (B:/~BUN/root/src/entrypoints/cli.js:4500:12874)\n    at processTicksAndRejections (native:7:39)","timestamp":"2026-04-12T09:22:08.923Z"},{"error":"Error: ENOENT: no such file or directory, unlink 'C:\\Users\\yossi\\AppData\\Local\\Temp\\claude\\C--Users-yossi-PycharmProjects-PythonProject2\\8b06513c-bb53-42c0-89b7-4f6985686345\\tasks\\a63247750a14a7047.output'\n    at async <anonymous> (B:/~BUN/root/src/entrypoints/cli.js:7823:299)","timestamp":"2026-04-12T09:39:27.850Z"}]