Uploading a large local file via galaxy_upload_file times out (MCP error -32001) and appears to kill the MCP connection

Uploading a local FASTQ from the user's machine repeatedly failed:

```
galaxy_upload_file: Failed to call tool: MCP error -32001: Request timed out
```

The upload of a large local file takes longer than the MCP client's request timeout, so the call is aborted before Galaxy finishes ingesting it. `galaxy_upload_file_from_url` (server-side fetch) works fine in the same sessions -- it's specifically the local-path upload that times out.

Notably, right after the upload timeouts the session degrades into a cascade of `Not connected` errors (see #199) -- the long, timed-out request looks like it desyncs/kills the stdio transport. So this is both its own blocker (can't upload large local files) and a likely trigger for #199.

Expected: a longer/streaming timeout for upload operations (or chunked/async upload).

App 0.3.1, deepseek-v4-flash, macOS. Related: #199.