fix: fix source ordering issue in manifest generation for multi-source app while using manifests and diff commands

[ishitasequeira]

Fixes #18359.

To be cherry-picked in release-2.11.

Checklist:

• Either (a) I've created an enhancement proposal and discussed it with the community, (b) this is a bug fix, or (c) this does not need to be in the release notes.
• The title of the PR states what changed and the related issues number (used for the release note).
• The title of the PR conforms to the Toolchain Guide
• I've included "Closes [ISSUE #]" or "Fixes [ISSUE #]" in the description to automatically close the associated issue.
• I've updated both the CLI and UI to expose my feature, or I plan to submit a second PR with them.
• Does this PR require documentation updates?
• I've updated documentation as required by this PR.
• I have signed off all my commits as required by DCO
• I have written unit and/or e2e tests for my change. PRs without these are unlikely to be merged.
• My build is green (troubleshooting builds).
• My new feature complies with the feature status guidelines.
• I have added a brief description of why this PR is necessary and/or what this PR solves.
• Optional. My organization is added to USERS.md.
• Optional. For bug fixes, I've indicated what older releases this fix should be cherry-picked into (this may or may not happen depending on risk/complexity).

[codecov]

Codecov Report

Attention: Patch coverage is 60.00000% with 2 lines in your changes are missing coverage. Please review.

Project coverage is 44.94%. Comparing base (a95d595) to head (0043867).
Report is 1 commits behind head on master.

Files	Patch %	Lines
server/application/application.go	60.00%	2 Missing ⚠️

Additional details and impacted files

@@           Coverage Diff           @@
##           master   #18395   +/-   ##
=======================================
  Coverage   44.94%   44.94%           
=======================================
  Files         354      354           
  Lines       47739    47740    +1     
=======================================
+ Hits        21454    21455    +1     
  Misses      23482    23482           
  Partials     2803     2803           

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[alexmt]

LGTM. thank you!

[ishitasequeira]

/cherry-pick release-2.11