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fix(filesystem): merge MCP roots with CLI-provided directories instead of replacing them #3616

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fix(filesystem): merge MCP roots with CLI-provided directories instead of replacing them #3616

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4 changes: 3 additions & 1 deletion src/filesystem/index.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -706,7 +706,9 @@ server.registerTool(
async function updateAllowedDirectoriesFromRoots(requestedRoots: Root[]) {
const validatedRootDirs = await getValidRootDirectories(requestedRoots);
if (validatedRootDirs.length > 0) {
allowedDirectories = [...validatedRootDirs];
// Merge with existing CLI-provided directories instead of replacing
const merged = new Set([...allowedDirectories, ...validatedRootDirs]);
allowedDirectories = [...merged];
setAllowedDirectories(allowedDirectories); // Update the global state in lib.ts
console.error(`Updated allowed directories from MCP roots: ${validatedRootDirs.length} valid directories`);
} else {
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