User Story

As a user,
I want a tool for removing files,
so that the LLM can manage the filesystem directly from within Tomo without escaping into run_command rm.

Acceptance Criteria

Tool shape

• New remove_file tool registered alongside existing tools at src/tools/remove-file.ts, follows existing tool patterns (zod schema, Tool interface, colocated test file, registered in src/app.tsx)
• Arguments: path (required, absolute or relative to cwd)
• Tool description explains: only removes files (not directories), use remove_dir for directories, fails clearly on missing path or directory path
• formatCall returns the path for the collapsed tool header
• New entry in toolsSchema in src/config/schema.ts so the tool can be enabled/disabled (default enabled: true)

Permissions

• New permission keys added to permissionsSchema in src/config/schema.ts:
  • cwdRemoveFile (default false) — allows removing files within the cwd without confirmation
  • globalRemoveFile (default false) — allows removing files outside the cwd without confirmation
• Permission check uses the existing isPathWithinCwd helper from src/tools/permissions.ts
• Permission resolution mirrors the existing read/write pattern: granted → skip confirm, ungranted → prompt
• Either extend checkFilePermission with a "remove" operation type or add a parallel helper — implementer's call, just keep the shape consistent with the existing read/write logic

Confirmation

• When permission is not granted, the confirmation prompt shows the resolved file path (label "Remove file?")
• User denial returns a denied result; flow follows the same pattern as write-file.ts

Validation and behaviour

• Errors clearly when the path does not exist
• Errors clearly when the path is a directory (suggest remove_dir)
• Errors clearly on permission/IO errors from the OS
• On success, returns a plain ok result confirming the path was removed

Tests

• Mock the filesystem at the boundary; do not mock internal helpers
• Tool behaviour: removes a file in cwd, removes a file outside cwd, errors on missing path, errors on directory path
• Permissions matrix: cwd granted skips confirm, cwd ungranted prompts and on approval removes, cwd ungranted prompts and on denial returns denied and leaves the file in place; same set of cases for global
• Confirmation prompt shape matches the existing pattern (label, detail)

Additional Context

run_command rm already covers this case but at the cost of shell quoting, cross-platform inconsistency, and a confirmation prompt on every call that doesn't match allowedCommands. A dedicated remove_file tool with its own permission gate gives cleaner ergonomics for the common refactor/rename workflow and lets the user grant cwd-scoped trust for file removal without having to allowlist rm patterns globally.

Pairs with #251 (remove_dir). Together they cover the destructive filesystem operations the LLM currently has to do via run_command.

Implementation references:

• src/tools/write-file.ts for the permission + confirm flow shape
• src/tools/permissions.ts for checkFilePermission and isPathWithinCwd
• src/config/schema.ts:19 for the permissions schema where the new keys go