Add public repository reanalysis workflow

[htsugawa]

Summary

• add repository adapters for Metabolomics Workbench, MetaboLights, and MB-POST
• select lightweight untargeted GC-MS and scan-based LC-MS projects reproducibly
• add a visual repository metadata handler that preserves source values and projects a user-defined field hierarchy into the single MS-DIAL Class column
• expose repository metadata inspection, class projection, and reviewed metadata export through the CLI, HTTP agent API, MCP server, and guided-analysis skill
• retain repository and publication provenance, reviewed sample metadata, MS-DIAL import metadata, methods, peak/alignment/mzTab-M outputs, and checksums after raw-data cleanup
• archive .dcl, .arf, .arf2, and .mdproject files into an integrity-checked ZIP before cleanup
• add bounded download leases, checksum verification, safe archive extraction, raw metadata preflight, and validation-gated cleanup
• recognize Shimadzu LCD/QGD inputs and make guided workflows resilient to stale saved resource paths
• document pilot selection, metadata review, artifact retention, and end-to-end reanalysis results

Validation

• 90 Python tests passed
• Python compile, JavaScript syntax, and git diff --check passed
• browser-tested repository metadata inspection, hierarchy selection, and Class preview with ST002419
• verified detailed metadata extraction with ST002419, MTBLS341, and MPST000007
• MTBLS341: mzTab-M passed with 410 SML/SMF rows
• ST002419: mzTab-M passed with 823 SML/SMF rows
• MPST000007: mzTab-M passed with 2448 SML/SMF rows
• raw leases were removed only after validated outputs and publication artifacts were retained

Dependency

• stacked on Probe MS-DIAL Console through standard command help #6 because this branch was developed from the Console help compatibility changes