Orbit/Galaxy MCP: no way to build a paired-end dataset collection

While setting up an RNA-seq run, a tester's agent tried to create a paired-end dataset collection by invoking a Galaxy builtin (`__BUILD_LIST_OF_PAIRS__`) through run_tool, got "Tool not found," and fell back to manual instructions in the Web UI. There's no MCP tool for building list/paired collections, so collection creation -- a routine prerequisite for most workflows -- isn't reachable programmatically.

This is a galaxy-mcp tool-surface gap; tracking here since that's where testers feel it. One of a small set of "missing Galaxy operation" reports filed together -- see siblings for Data Libraries, workflow import, and dataset purge.

---
Filed together as the missing-Galaxy-operation set: #226 (Data Libraries), #227 (workflow import), #228 (dataset purge), #229 (paired-collection build).

Start by tracing how run_tool exposes Galaxy operations, then compare its handling of the __BUILD_LIST_OF_PAIRS__ builtin with the existing tool surface. The work is done when an MCP caller can create a paired-end dataset collection programmatically instead of falling back to the Web UI.

Written by the indexing model from the issue text.