[breaking] Remove indexes v2 endpoint

[umbynos]

Please check if the PR fulfills these requirements

• The PR has no duplicates (please search among the Pull Requests
  before creating one)
• Tests for the changes have been added (for bug fixes / features)

• What kind of change does this PR introduce?

removal of indexes endpoint ("/v2/pkgs/indexes")

• What is the current behavior?

The indexes endpoint is not used and is a security risk, we are going to remove it

• What is the new behavior?

Index endpoint is not there anymore.

I took the opportunity to refactor a bit how the "package_staging_index.json" is treated. Now it's handled in the index package and is used by both the old implementation and the new GOA one.

• Does this PR introduce a breaking change?

Yes, but the endpoint should not be used

• Other information:

[codecov-commenter]

Codecov Report

Attention: 101 lines in your changes are missing coverage. Please review.

Comparison is base (bf32bad) 18.37% compared to head (5f0a64c) 19.09%.

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #838      +/-   ##
==========================================
+ Coverage   18.37%   19.09%   +0.71%     
==========================================
  Files          53       46       -7     
  Lines        4120     3635     -485     
==========================================
- Hits          757      694      -63     
+ Misses       3257     2850     -407     
+ Partials      106       91      -15     

Flag	Coverage Δ
unit	19.09% <45.69%> (+0.71%)	⬆️

Flags with carried forward coverage won't be shown. Click here to find out more.

Files	Coverage Δ
index/hidefile_default.go	100.00% <100.00%> (ø)
tools/shell_default.go	0.00% <ø> (ø)
v2/http.go	81.48% <100.00%> (-6.02%)	⬇️
v2/pkgs/tools.go	72.51% <97.43%> (+3.69%)	⬆️
main.go	2.30% <0.00%> (+<0.01%)	⬆️
tools/download.go	35.90% <0.00%> (+6.46%)	⬆️
tools/tools.go	0.00% <0.00%> (ø)
index/index.go	52.50% <52.50%> (ø)

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[alessio-perugini]

I've tested on Linux and it works flawlessly. 🚀
Do you mind testing it on Windows? (Just to be sure that the hideFile function still behaves correctly.)

Great job! Slowly making the agent great again! 😎

[alessio-perugini]

LGTM.
nit: remove redundant getters methods from the tools struct

[umbynos]

Just rebased to include changes from #836