fix: dependency removal when multiple dependencies exist (#429)

[Vasist10]

Description

Fix implemented:

• Explicitly clear all existing dependencies using depends:

• Re-apply the updated dependency list to ensure the final state matches the request

• Added a regression test to cover multi-dependency removal and prevent future regressions

• Fixes: bug: Removing dependencies fails when multiple dependencies exist #428

Checklist

• Ran npx prettier --write . (for formatting)
• Ran gofmt -w . (for Go backend)
• Ran npm test (for JS/TS testing)
• Added unit tests, if applicable
• Verified all tests pass
• Updated documentation, if needed

Additional Notes

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