Manifest annotations where not copied to index

[jonesbusy]

Small issue I discovered comparing the java and go implementation

Test were indeed wrong

Manifest annotations where not copied to index

And added some cleanup

Description

Testing done

Submitter checklist

• I have read and understood the CONTRIBUTING guide
• I have run mvn license:update-file-header, mvn spotless:apply, pre-commit run -a, mvn clean install before opening the PR

[codecov]

Codecov Report

Attention: Patch coverage is 83.33333% with 2 lines in your changes missing coverage. Please review.

Project coverage is 85.41%. Comparing base (38220a8) to head (8bdd0a0).
Report is 2 commits behind head on main.

Files with missing lines	Patch %	Lines
src/main/java/land/oras/Index.java	71.42%	1 Missing and 1 partial ⚠️

Additional details and impacted files

@@             Coverage Diff              @@
##               main     #218      +/-   ##
============================================
- Coverage     85.43%   85.41%   -0.02%     
- Complexity      450      453       +3     
============================================
  Files            33       33              
  Lines          1497     1502       +5     
  Branches        173      174       +1     
============================================
+ Hits           1279     1283       +4     
  Misses          144      144              
- Partials         74       75       +1     

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