fix: Prune dotfiles rather than ignore, make --prune inject default ignores into prune list

[effigies]

Initially narrowly scoped to prune .git, this PR now includes the following changes:

• Dotfiles and directories are now pruned during walk, rather than ignored after the walk. This saves descent into .git/ or other potentially deep hidden directories (.venv/, for example).
• --prune now injects the default ignore list into the prune list, which is a more principled way to decide what gets pruned.
• To preserve the original intended behavior of --prune, derivatives/ is now ignored.
• To avoid pruning .bidsignore and causing --prune to un-ignore everything, .bidsignore is now ignored through a carve-out in the BIDSFile.ignored property. As a validator feature and not a BIDS feature, this seems reasonable to me.
• The file tree builders now all construct a default prune list for consistency.

Open issues (probably for separate PRs):

• Generating the default ignore list from schema. There's a bit of a chicken and egg problem where if the ignore list comes from a newer schema than is declared in dataset_description.json, we're not respecting that, but that's already the case. We already don't load the schema based on dataset_description.json, so as long as we load it from --schema, we're still improving.
• The file count skips ignored files... With significant confounds like .git now being pruned instead of ignored, I think it may be time to revisit this and count ignored files for a more accurate description of dataset size.

Closes #412.

[codecov]

Codecov Report

❌ Patch coverage is 88.57143% with 4 lines in your changes missing coverage. Please review.
✅ Project coverage is 87.35%. Comparing base (1d21e18) to head (c70a5d6).
⚠️ Report is 1 commits behind head on main.

Files with missing lines	Patch %	Lines
src/main.ts	0.00%	4 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #413      +/-   ##
==========================================
- Coverage   87.37%   87.35%   -0.02%     
==========================================
  Files          65       65              
  Lines        4777     4794      +17     
  Branches      781      780       -1     
==========================================
+ Hits         4174     4188      +14     
- Misses        510      513       +3     
  Partials       93       93              

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[effigies]

@yarikoptic Care to give this branch a try?

[effigies]

Well, this turned into a rabbit hole. Will try again later.

[effigies]

PR description updated. I cast the review net a bit wider, since this is a fairly significant change.

[rwblair]

I'm waffling on how transparent we should be with what exactly is pruned when the --prune option isn't used or is false. The defaults are sensible so I don't think we'll surprise any one, but my lack of imagination has tied my shoelaces together before.

Should the contents of ignoreDefaults be more visible in help text or documentation?

Do you think a logger.info readout of pruned files would be useful to anyone?

The nomeclature/semantics of --prune feels strange sometimes, but something like --extended-prune feels worse, so I'm fine with keeping it for now.

[rwblair]

This may need to be added to the help text for the flag.