GSA correctness fixes (review, area 2)

[adamjohnwright]

These come from the max-level review of the chat flow. Each was reproduced by the reviewer.

Finding	Fix	Test
group1/group2 came from a case-sensitive sorted(), so the baseline depended on spelling	The first label given is group 1, and the result says what was compared	Four label orders. Sabotaged.
An R write.table header (no gene-column cell) lost its first sample	A header one cell short of the rows is all sample names	Unit test. Sabotaged.
CSV uploads were submitted unconverted, and the service reads tabs only	Matrix.text returns tab-separated text	Unit test (quoted comma field), and in the browser
The strict decode at submit didn't match the lenient decode at validation, so Windows files passed validation and then failed every retry	One decode() for both: UTF-8 (with BOM), UTF-16, Windows-1252	cp1252 and UTF-16 tests
Validation was unbounded and ran on the event loop: 21M blank lines, or a 7M-column header	1,000 samples at most; blank lines count towards the read limit; validate and the matrix read run via to_thread	Too-many-columns test; 3M blank lines decided in under 1s
One 502 or timeout while polling lost a finished run	Up to 4 tries per request. The failure message gives the analysis id.	Survives 2 failures (fixed count). A lasting outage still ends the wait. Sabotaged.

Browser

run_flow.py ran against a stand-in ReactomeGSA that replays the recorded service responses and records what the chat submits. Two runs: the melanoma TSV, and the same matrix as a CSV. Both submitted tab-separated data with 16 samples and {"group1": "MOCK", "group2": "MCM"}, finished, and offered the 2,679-row table to download. The result reads "Compared: MOCK (group 1, the first label you gave) with MCM (group 2)."

Not changed

• Direction sign. ReactomeGSA's documentation doesn't say which way its Direction points, so the chat doesn't claim it.
• Data type. Uploads are still always submitted as rnaseq_counts; the review rated this medium. Proteomics and microarray uploads need asking which kind of data the reader has.
• JSON encoding. The 20 MB JSON body at submit is still encoded on the event loop (0.3–0.6s).

./checks.sh passes.

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