refactor(commands): extract cross-cutting commands from files.py

[ypriverol]

Summary

Follow-up to #101. Extracts the three cross-cutting commands (download_files_by_url, download_files_by_list, download_px_raw_files and their helpers) from pridepy/files/files.py into a new pridepy/commands/ package. No behaviour change.

files.py size: 1254 → 995 LOC (21% reduction). The spec target of <700 LOC was overly optimistic; the remaining 995 is largely backward-compat shims for the ~40 methods that tests patch via Files.X. Migrating tests to patch the new modules directly would let the shims be removed, but that's deferred to a separate PR.

What moved

Old location	New location
Files.download_px_raw_files + _normalize_px_xml_url + _parse_px_xml_for_raw_file_urls	commands/proteomexchange.py (94 LOC)
Files.download_files_by_list	commands/by_list.py (58 LOC)
Files.download_files_by_url + 6 URL helpers (_extract_pride_accession, _validate_urls_checksums, _http_download_url, _ftp_download_url, _dispatch_url_scheme, _download_single_url)	commands/by_url.py (254 LOC)

Backward compatibility

Files keeps shim staticmethods for every moved function. Tests use patch.object(Files, "_http_download_url") and patch.object(Files, "_download_single_url") — both still intercept because the new commands/by_url.py internal helpers route through Files.X (lazy import) for the patch-sensitive ones.

Tests

68 passed, 4 skipped — same as PR #101 baseline. No assertion changes.

Verification

• Live smoke test: pridepy download-file-by-name -a MSV000080175 -f params.xml produces MD5 43d87368d705c3f380c1d030b14850c4 (matches the pre-refactor baseline).
• All 8 test_download_resilience.py tests pass.
• All 4 test_download_by_url.py tests pass (the ones patching Files._http_download_url, _ftp_download_url, _download_single_url).
• All 9 test_download_by_list.py tests pass.

Base-branch note

This PR targets refactor/files-py-providers (PR #101) so the diff is small. Once #101 merges to dev, update this PR's base.

Test plan

• CI passes
• wc -l pridepy/files/files.py reports < 1000
• Smoke test: pridepy download-file-by-name -a MSV000080175 -f params.xml produces MD5 43d87368d705c3f380c1d030b14850c4

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[ypriverol]

Superseded by #103, which consolidates PR #100, #101, and #102 into a single branch (feat/files-py-modular-architecture) targeting dev. All 4 commits from this PR are preserved verbatim in #103. Please review and merge there instead.