Name the --overwrite flag in file-exists errors

[bendichter]

Fixes #748.

The "already exists" errors raised by save_report and by the CLI for --json-file-path told the user to pass -o, which is not a flag the CLI defines. Both now say --overwrite.

One test calls save_report against an existing file and matches on --overwrite; the other drives the CLI with click's CliRunner against an existing JSON path and checks the exception text. Both fail on dev.

🤖 Generated with Claude Code

https://claude.ai/code/session_01Hfn8dhw9cwP5FiVaCgFmCt

[h-mayorquin]

The fix is good, thanks for catching this (the message was sending people to a flag that errors out!).

One thing we could improve here. Both existence checks run after the whole inspection is done. The json_file_path one is after messages = list(messages_iterator) and the save_report one is later still, and neither of them needs the messages, they are only looking at a path. If we move them up to the top with the rest of the argument handling then a user who points --json-file-path at a file that already exists finds out right away instead of after scanning a whole dandiset.

That would also make test_cli_existing_json_file_message_names_overwrite_flag a lot lighter. Right now it writes an NWB file with NWBHDF5IO and runs the whole CLI to check a substring, and with the check at the top it does not need a file at all.

[bendichter]

Good call. Both checks now run with the rest of the argument handling, before anything is inspected, and they cover --report-file-path as well as --json-file-path. The late check on the JSON path is gone since it could no longer fire; the one inside save_report stays for callers of the library. The CLI tests now point the command at an empty folder, so no NWB file is written, and there is a third test that runs with --overwrite to confirm both files are then rewritten.

[h-mayorquin]

LGTM, thanks for addressing the feedback.

[codecov-commenter]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 88.90%. Comparing base (e5001c1) to head (1d386e8).
⚠️ Report is 4 commits behind head on dev.

Additional details and impacted files

@@            Coverage Diff             @@
##              dev     #749      +/-   ##
==========================================
+ Coverage   81.26%   88.90%   +7.64%     
==========================================
  Files          48       48              
  Lines        1916     1938      +22     
==========================================
+ Hits         1557     1723     +166     
+ Misses        359      215     -144     

Files with missing lines	Coverage Δ
src/nwbinspector/_formatting.py	83.44% <100.00%> (+13.10%)	⬆️
src/nwbinspector/_nwbinspector_cli.py	78.16% <100.00%> (+78.16%)	⬆️

... and 4 files with indirect coverage changes

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