fix(pdf-server): keep CLI-arg directories across client roots refreshes

[cpruijsen]

Fixes #644. Directories passed as CLI args to pdf-server now survive a client roots refresh.

refreshRoots() in examples/pdf-server/server.ts cleared allowedLocalDirs on every successful listRoots(). In --stdio mode useClientRoots is always on, so a host that advertises roots but returns an empty list wiped every CLI-arg directory. After that, list_pdfs reported allowedDirectories: [] and display_pdf rejected all local paths.

Fix

main() now also records CLI-arg directories in a new cliLocalDirs set, following the existing cliLocalFiles pattern. refreshRoots() re-adds them right after the clear. Client roots keep clear-and-replace semantics, so a root the client removes is still revoked.

The issue suggests either clearing only on a non-empty list or dropping the clear. Both stop the client from revoking roots: the first for its last root, the second for any root. A provenance set protects only the launch-time grants. If you prefer the smaller non-empty check, I can switch to it.

Tests

Two new tests in examples/pdf-server/server.test.ts run the real initialize handshake over InMemoryTransport with a client that declares roots:

• An empty roots/list at init keeps the CLI directory and drops a directory from an earlier refresh.
• A root removed via notifications/roots/list_changed is revoked, and the CLI directory stays.

Both fail without the re-add in refreshRoots() and pass with it.

Not in this PR

A comment on the issue reports that fileUrlToPath() turns file:///C:/x into /C:/x, so Windows file roots are dropped. That is a separate bug. With this PR, CLI-arg directories survive on Windows, but client roots there still need that fix.