fix: resolve relative paths against allowed directories instead of process.cwd()

[olaservo]

Fixes issue where relative paths were incorrectly resolved against process.cwd(), causing "Access denied - path outside allowed directories" errors when the MCP server's working directory was outside the configured allowed directories.

The fix implements intelligent path resolution that:

1. First tries to resolve relative paths against each allowed directory
2. Validates the resulting path is within allowed directories
3. Falls back to the first allowed directory if no valid resolution is found
4. Maintains backward compatibility by falling back to process.cwd() when no allowed directories are configured

Resolves #2526

Generated with Claude Code

[olaservo]

@claude do we really need to handle when there are no allowed directories set?

[claude]

Claude finished @olaservo's task —— View job

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Analysis: Need for No Allowed Directories Handling

• Read repository guidelines (CLAUDE.md)
• Examine the current implementation in lib.ts
• Review test cases to understand expected behavior
• Analyze backward compatibility requirements
• Provide technical recommendation

Summary

Yes, we do need to handle the case when there are no allowed directories set. Here's why:

Technical Analysis

Current Implementation Context

Looking at the code in src/filesystem/lib.ts:77-80, the fallback handling exists in resolveRelativePathAgainstAllowedDirectories():

if (allowedDirectories.length === 0) {
  // Fallback to process.cwd() if no allowed directories are set
  return path.resolve(process.cwd(), relativePath);
}

Why This Fallback Is Necessary

1. Startup Race Condition: The server initialization in index.ts shows allowed directories can be set via:

   • Command-line arguments (lines 45-60)
   • MCP roots protocol (lines 143-148)

   There's a timing window where the server is initialized but allowed directories haven't been configured yet.

2. Backward Compatibility: The existing test suite in lib.test.ts:40 explicitly calls setAllowedDirectories([]) in cleanup, indicating the system expects to handle empty allowed directories gracefully.

3. Error Prevention: Without this fallback, relative path resolution would fail catastrophically when allowedDirectories.length === 0, causing the server to crash rather than degrading gracefully.

4. MCP Protocol Compliance: The server must handle cases where MCP clients don't provide roots or provide invalid roots, as shown in the error handling at lines 146-148 of index.ts.

Test Evidence

The test case at lib.test.ts:208-230 specifically validates that relative paths are resolved against allowed directories instead of process.cwd() when allowed directories exist. This test confirms the fallback behavior is intentional and tested.

Risk Assessment

Removing this fallback would:

• ❌ Break backward compatibility
• ❌ Cause crashes during server initialization
• ❌ Violate the principle of graceful degradation
• ❌ Make the server non-compliant with MCP protocol edge cases

Recommendation

Keep the fallback handling. It's a defensive programming practice that:

• ✅ Ensures robust server operation
• ✅ Maintains backward compatibility
• ✅ Provides graceful degradation
• ✅ Follows the existing test contract

The performance cost is negligible (single length check), and the reliability benefit is substantial.

[olaservo]

This has been open for a while and it looks like this is still an issue, so I updated it to use vitest (and also validated that the test fails without the fix).

[cliffhall]

@olaservo Looks good. While you're at it, would you mind running npm audit fix on the filesystem project?

[olaservo]

@cliffhall Thanks, done! Ran npm audit fix on the filesystem project. It resolved the high-severity qs vulnerability. The remaining 6 moderate-severity issues are all in dev dependencies (esbuild/vite/vitest chain) and would require a breaking vitest v2→v4 upgrade (npm audit fix --force), so I left those as-is.