fix: file permission issue in e2e tests & regression on db init

[coopernetes]

Closes #1354

Two fixes to e2e tests as well as a regression caused by the app
initialization.

• pullRemote - Error: EACCES: permission denied, mkdir './.remote' errors during e2e test runs (Dockerfile fix of file permissions)
• Fix issue where getAllProxiedHosts() does not complete until after the Express router starts up, leading the git-server:8443 origin to not be proxied (regression from fix: defer reading of database configuration until needed to fix race #1316) which causes the proxy to default to github.com. The following logs are observed in the git-proxy container:

$ docker compose logs git-proxy
Created runtime configuration with:
  API URL: auto-detect
  Allowed Origins: *
  Environment: test
Configuration sources are disabled
Configuration loaded successfully
Setting config file to: /app/test-e2e.proxy.config.json
validating config
Setting up the proxy and Service
No plugins configured
Found 0 plugin modules
Loading MongoDB database adaptor
creating new repo {"project":"coopernetes","name":"test-repo","url":"https://git-server:8443/coopernetes/test-repo.git","users":{"canPush":[],"canAuthorise":[]}}
creating new repo {"project":"finos","name":"git-proxy","url":"https://git-server:8443/finos/git-proxy.git","users":{"canPush":[],"canAuthorise":[]}}
Initializing proxy router for origins: '[]'
        setting up catch-all route (github.com) for backwards compatibility
        
       # !!! Note how git-server:8443 is never added as a proxied origin ^
...
checkRepoInAuthorisedList - repo https://git-server:8443/coopernetes/test-repo.git is in the authorisedList
Action processed: Allowed
    Request URL: /git-server:8443/coopernetes/test-repo.git/info/refs?service=git-upload-pack
    Host:        localhost:8000
    User-Agent:  git/2.52.0
Request resolved to https://github.com/git-server:8443/coopernetes/test-repo.git/info/refs?service=git-upload-pack

       # !!! Request incorrectly proxied to github.com instead of git-server:8443 ^

[netlify]

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[github-actions]

Dependency Review

✅ No vulnerabilities or license issues or OpenSSF Scorecard issues found.

Scanned Files

None

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 80.40%. Comparing base (930a5da) to head (36781fd).
⚠️ Report is 3 commits behind head on main.

Additional details and impacted files

@@           Coverage Diff           @@
##             main    #1358   +/-   ##
=======================================
  Coverage   80.40%   80.40%           
=======================================
  Files          65       65           
  Lines        4608     4608           
  Branches      776      775    -1     
=======================================
  Hits         3705     3705           
  Misses        888      888           
  Partials       15       15           

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[coopernetes]

/test e2e