ignore client roots by default in pdf-server (#510)

* security: ignore client roots by default in pdf-server

When the pdf-server is started with --stdio, MCP clients may advertise
roots that refer to directories on the *client's* file system. Because
the server resolves those paths locally, accepting them by default would
give the remote client access to arbitrary directories on the server's
machine.

This commit makes client roots opt-in via the --use-client-roots flag.
Without the flag, the server logs a notice and skips roots setup
entirely. The createServer() function now accepts a CreateServerOptions
object with a `useClientRoots` boolean (defaults to false).

https://claude.ai/code/session_014ohk5NMEPe8TBKpqp4ZRSw

* Enable client roots by default for HTTP, keep off for stdio

HTTP mode serves a local client so roots are safe. Stdio mode may
have a remote client whose roots would resolve against the server's
filesystem, so roots stay off unless --use-client-roots is passed.

https://claude.ai/code/session_014ohk5NMEPe8TBKpqp4ZRSw

* fix: correct transport-aware defaults for useClientRoots

stdio = local client (e.g. Claude Desktop) → auto-enable roots
HTTP = remote client → ignore roots unless --use-client-roots passed

The previous commit had the logic inverted.

https://claude.ai/code/session_014ohk5NMEPe8TBKpqp4ZRSw

* refactor: inline useClientRoots per transport branch

Remove the intermediate effectiveUseClientRoots variable — just pass
`true` in the stdio branch and the flag value in the HTTP branch.

https://claude.ai/code/session_014ohk5NMEPe8TBKpqp4ZRSw

* docs: update README to match transport-aware client roots defaults

Stdio always enables roots (client is local); HTTP ignores them by
default. The previous README text had these reversed.

https://claude.ai/code/session_014ohk5NMEPe8TBKpqp4ZRSw

---------

Co-authored-by: Claude <noreply@anthropic.com>

examples/pdf-server/README.md

@@ -149,9 +149,27 @@ bun examples/pdf-server/main.ts ./local.pdf https://arxiv.org/pdf/2401.00001.pdf
 bun examples/pdf-server/main.ts --stdio ./papers/
 ```
 
+## Security: Client Roots
+
+MCP clients may advertise **roots** — `file://` URIs pointing to directories on the client's file system. The server uses these to allow access to local files under those directories.
+
+- **Stdio mode** (`--stdio`): Client roots are **always enabled** — the client is typically on the same machine (e.g. Claude Desktop), so the roots are safe.
+- **HTTP mode** (default): Client roots are **ignored** by default — the client may be remote, and its roots would be resolved against the server's filesystem. To opt in, pass `--use-client-roots`:
+
+```bash
+# Trust that the HTTP client is local and its roots are safe
+bun examples/pdf-server/main.ts --use-client-roots
+```
+
+When roots are ignored the server logs:
+
+```
+[pdf-server] Client roots are ignored (default for remote transports). Pass --use-client-roots to allow the client to expose local directories.
+```
+
 ## Allowed Sources
 
-- **Local files**: Must be passed as CLI arguments
+- **Local files**: Must be passed as CLI arguments (or via client roots when enabled)
 - **Remote URLs**: arxiv.org, biorxiv.org, medrxiv.org, chemrxiv.org, zenodo.org, osf.io, hal.science, ssrn.com, and more
 
 ## Tools