fix(filesystem): preserve CLI directories when merging with MCP roots

[Bingtagui404]

Summary

Fixes #3602

When the MCP client supports the roots protocol, the oninitialized and roots/list_changed handlers unconditionally replaced all CLI-provided allowedDirectories with client roots. This caused any extra directories passed via command-line arguments to be silently discarded.

Before: npx @modelcontextprotocol/server-filesystem /home/user /mnt/Storage /mnt/Games + client root /home/user → only /home/user accessible.

After: CLI directories are preserved as an immutable baseline and merged with client roots. All four directories remain accessible.

Changes

• src/filesystem/index.ts: Save CLI directories as cliAllowedDirectories baseline. Change updateAllowedDirectoriesFromRoots to merge CLI baseline + current client roots instead of replacing. When roots become empty/invalid, fall back to CLI baseline only (no stale roots).
• src/filesystem/roots-utils.ts: Add mergeAllowedDirectories() helper — uses Set to deduplicate CLI dirs + root dirs.
• src/filesystem/__tests__/roots-utils.test.ts: Add 3 regression tests:
  • Preserves CLI directories while adding current client roots
  • Deduplicates directories shared by CLI args and client roots
  • Falls back to CLI baseline when client provides no valid roots

Test plan

• npx tsc --noEmit — type check passes
• npx vitest run --config src/filesystem/vitest.config.ts src/filesystem/__tests__/roots-utils.test.ts — all 6 tests pass (3 existing + 3 new)
• Full filesystem test suite — no new failures introduced

[Bingtagui404]

Filesystem checks are passing for this PR. The only failing job is Build fetch, which appears unrelated to the files changed here. I've pushed a no-op commit to retrigger CI.

[Bingtagui404]

Filesystem-related checks are passing for this PR. The failing Build fetch job is unrelated to this change: it fails during uv sync --locked --all-extras --dev because src/fetch/uv.lock needs to be updated. The same Build fetch failure is also present on the current main branch (run #23161383338).

[Bingtagui404]

To clarify: the Build fetch failure is a known repo-wide issue tracked in #3548. It is unrelated to the filesystem changes in this PR.