Fix vault .gitignore creation for existing directories

[shunichironomura]

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Summary

• ensure the vault directory exists without returning before .gitignore setup
• atomically create .gitignore only when absent, preserving existing custom contents
• add regression coverage for pre-existing vault directories and existing ignore files

Closes #1072.

AI assistance

• AI used: yes — Amp investigated the issue, implemented the fix, and added tests
• Human review of AI-assisted code: pending

Breaking changes

• No breaking changes
• Breaking changes; the breaking change label is applied

[codecov-commenter]

Codecov Report

❌ Patch coverage is 90.32258% with 3 lines in your changes missing coverage. Please review.
✅ Project coverage is 54.42%. Comparing base (433b438) to head (f204887).

Files with missing lines	Patch %	Lines
crates/capsula-core/src/run.rs	90.32%	3 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #1222      +/-   ##
==========================================
+ Coverage   54.16%   54.42%   +0.25%     
==========================================
  Files          44       44              
  Lines        4233     4257      +24     
==========================================
+ Hits         2293     2317      +24     
  Misses       1940     1940              

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