Fix failure in updating GIT index of cargo registry server

[pgarg66]

Problem

The cargo registry server fails to start if the index configuration changes (e.g. due to change in port or IP address)

thread 'main' panicked at cargo-registry/src/dummy_git_index.rs:80:18:
Failed to get tree: Error { code: -1, klass: 14, message: "failed to insert entry: invalid object specified - git" }
note: run with `RUST_BACKTRACE=1` environment variable to display a backtrace

Summary of Changes

The config change requires a new commit to the GIT index. The staging of the commit was adding all the files, including .git folder. That was causing the issue. This PR adds only the required files to the stage/commit.

Fixes #

[codecov]

Codecov Report

Merging #33628 (b326da1) into master (1d91b60) will increase coverage by 0.1%.
Report is 17 commits behind head on master.
The diff coverage is 91.4%.

@@            Coverage Diff            @@
##           master   #33628     +/-   ##
=========================================
+ Coverage    81.7%    81.8%   +0.1%     
=========================================
  Files         807      807             
  Lines      218252   217896    -356     
=========================================
+ Hits       178438   178448     +10     
+ Misses      39814    39448    -366