fix(pdf-server): preserve CLI directories during roots refresh - #780

Summary

• track directories explicitly approved through CLI arguments separately from client-provided roots
• restore those CLI directories whenever the MCP roots allowlist is refreshed
• await the initial roots refresh so initialization has deterministic completion semantics
• add a regression test for a roots-capable client returning an empty root list

This prevents a client capability mismatch from silently removing directories the user explicitly supplied on the command line, while still allowing stale client-provided roots to be revoked.

Closes #644.

Verification

• bun test examples/pdf-server/server.test.ts — 90 passed, 2 platform-specific skipped
• npm run --workspace examples/pdf-server build
• repository pre-push verification — 439 passed, 2 platform-specific skipped; full build passed
• git diff --check