Fix #981: make generic_file.ext optional in generic_file schema

[claude]

Summary

Fixes #981. The 12 TestGeneFromFiles failures on main — every one of the form:

Required file "generic_file.ext" is declared in the file_list of
generic_file doc <id> but no file is bound to that name
(files.file_info has no entry for it)

— come from session.database_add(...) on a generic_file doc produced by ndi.fun.doc.gene.makeSourceFile under its default attachFile=false. DID-matlab's issue-#199 tightening (did.database.checkfiles at database.m:1710) now refuses this case that used to fall through to isvalid = 1.

The generic_file class is used in two legitimate modes:

• describe-only (the default): the doc records the source file's name and MD5 checksum without ingesting a copy — deliberate for the ~9.4 GB SAW .gef case, documented on makeSourceFile itself.
• attach (attachFile=true): the file is bound to the doc.

This PR flips mustbenotempty: 1 → mustbenotempty: 0 on the generic_file.ext file entry in generic_file_schema.json. Both modes validate cleanly under DID's tightened check:

• Step 1 (setdiff(expectedNames, actual_file_list)) still passes because the definition file continues to declare generic_file.ext in file_list.
• Step 3 (must-bind check) is now skipped for generic_file.ext; the attach path still binds it, the describe path is no longer refused.

This matches the pattern already used by pyraview_schema.json and the tile files in spatialGeneExpressionTiles_schema.json, which declare optional bindings with mustbenotempty: 0.

Options considered:

• A. Bind a placeholder in makeSourceFile — would satisfy the schema but would force testSourceFileDescribesWithoutIngestingAPayload to stop asserting verifyEmpty(doc.current_file_list()), which is exactly the documented invariant of the describe-only default.
• B (this PR). Loosen the schema — one-line change, no test churn, semantically correct because the class genuinely has two modes.
• C. Split into two classes — most churn; disproportionate for the fix.

The check being loosened only fired at write time on a doc whose file_list declared generic_file.ext but bound nothing. Since makeSourceFile is the only producer of generic_file docs in the codebase and its two branches are add_file(...) or nothing, there is no attach-path bug the required-file check was silently catching.

Expected effect on CI

All 12 previously-failing TestGeneFromFiles tests should pass:

• testPyramidTilesCarryTheSourceFileDependency
• testCellsCarryTheSourceFileDependency
• testFromGefBuildsTheWholeLadder
• testFromGefTakesTheChipAndPixelSizeFromTheFile
• testFromGefRecordsTheSourceFileByDefault
• testFromGefReportsProgressThroughTheWholeRun
• testFromGefWithoutAProgressFcnIsSilentRatherThanBroken
• testFromGefRefusesWithoutASubject (was reporting 'DID:Database:ValidationFiles' before fromGEF reached the subject-required check)
• testFromCellBinBuildsCellsAgainstThePyramid
• testFromCellBinRecordsWhatTheReaderConcludedNotWhatWasAsked
• testFromCellBinIngestsARequestedLabeling
• testFromCellBinTakesUnsupervisedFromTheCallerNotTheFile

The attachFile=true test (testSourceFileCanAttachWhenAsked) also continues to pass — the schema now permits the file binding rather than requiring it, and the code still binds when asked.

Once this lands, PR #979 will go green on rebase (its diff is orthogonal — lightsheet scaffold).

Test plan

• CI: Run NDI Test Suite No Cloud — expect the 12 TestGeneFromFiles failures to clear.
• Local reviewer with MATLAB: run ndi.unittest.fun.doc.gene.TestGeneFromFiles and confirm all pass.
• Static: no other producer of generic_file docs beyond makeSourceFile; the schema change does not affect docs that already bind a file.

🤖 Generated with Claude Code

https://claude.ai/code/session_01Cn7RipE1szEPizasFa1EEo

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Generated by Claude Code

[github-actions]

Test Results

1 295 tests  ±0   1 262 ✅ ±0   4m 34s ⏱️ +3s
  201 suites ±0      33 💤 ±0 
    1 files   ±0       0 ❌ ±0 

Results for commit 3eb8db8. ± Comparison against base commit 114e034.

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 29.19%. Comparing base (114e034) to head (3eb8db8).

Additional details and impacted files

@@           Coverage Diff           @@
##             main     #982   +/-   ##
=======================================
  Coverage   29.19%   29.19%           
=======================================
  Files         853      853           
  Lines       43037    43037           
=======================================
  Hits        12566    12566           
  Misses      30471    30471           

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