Fix package dependencies duplication

[akondas]

Fixes #468

[codecov]

Codecov Report

Merging #472 (2c026bd) into master (c15d282) will increase coverage by 0.00%.
The diff coverage is 100.00%.

@@            Coverage Diff            @@
##             master     #472   +/-   ##
=========================================
  Coverage     99.33%   99.33%           
- Complexity     1892     1893    +1     
=========================================
  Files           298      298           
  Lines          5971     5978    +7     
=========================================
+ Hits           5931     5938    +7     
  Misses           40       40           

Impacted Files	Coverage Δ
src/Entity/Organization/Package.php	100.00% <100.00%> (ø)
...ackageSynchronizer/ComposerPackageSynchronizer.php	97.12% <100.00%> (ø)

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