Improve LSP diagnostics handling for file operations

- Split LSP file notification into separate functions
- Add waitForLspDiagnostics function to wait for diagnostics after file changes
- Move LSP diagnostics to after file operations in edit and write tools
- Fix string splitting in diff generation
- Reduce diagnostics timeout from 10 to 5 seconds

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Co-Authored-By: termai <noreply@termai.io>