Updating docs to match the code.

[zrm22]

Description

Fixing doc consistency issues.

Type of change

What type of changes does your code introduce? Put an x in boxes that apply.

• CHANGE (fix or feature that would cause existing functionality to not work as expected)
• FEATURE (non-breaking change which adds functionality)
• BUGFIX (non-breaking change which fixes an issue)
• ENHANCEMENT (non-breaking change which improves existing functionality)
• NONE (if none of the other choices apply. Example, tooling, build system, CI, docs, etc.)

Checklist:

• I have performed a self-review of my code
• I have commented my code, particularly in hard-to-understand areas
• I have updated relevant documentation

Changelog entry

Please add a one-line changelog entry below. This will be copied to the changelog file during the release process.

Updating RopeBWT3 documentation consistency.

[codecov]

Codecov Report

Attention: Patch coverage is 57.14286% with 3 lines in your changes missing coverage. Please review.

Project coverage is 80.90%. Comparing base (3cb3fa8) to head (7d39558).
Report is 5 commits behind head on main.

Files with missing lines	Patch %	Lines
src/main/kotlin/net/maizegenetics/phgv2/cli/Phg.kt	0.00%	1 Missing ⚠️
...et/maizegenetics/phgv2/pathing/ropebwt/MapReads.kt	50.00%	0 Missing and 1 partial ⚠️
...aizegenetics/phgv2/pathing/ropebwt/RopeBwtIndex.kt	75.00%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #277      +/-   ##
==========================================
- Coverage   80.91%   80.90%   -0.02%     
==========================================
  Files          95       95              
  Lines        7159     7160       +1     
  Branches     1190     1191       +1     
==========================================
  Hits         5793     5793              
  Misses        906      906              
- Partials      460      461       +1     

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