Log warning when dependency graph is missing the root node

[nscuro]

Description

Logs a warning when dependency graph is missing the root node.

Also clean up code that is no longer necessary since Alpine v3, and apply consistent formatting for long method signatures.

Addressed Issue

Fixes #3989

Additional Details

N/A

Checklist

• I have read and understand the contributing guidelines
• This PR fixes a defect, and I have provided tests to verify that the fix is effective
• This PR implements an enhancement, and I have provided tests to verify that it works as intended~
• This PR introduces changes to the database model, and I have added corresponding update logic
• This PR introduces new or alters existing behavior, and I have updated the documentation accordingly

[codacy-production]

Coverage summary from Codacy

See diff coverage on Codacy

Coverage variation	Diff coverage
✅ +0.02% (target: -1.00%)	✅ 100.00% (target: 70.00%)

Coverage variation details

	Coverable lines	Covered lines	Coverage
Common ancestor commit (4420a9d)	22108	16887	76.38%
Head commit (2c9dd87)	22104 (-4)	16889 (+2)	76.41% (+0.02%)

Coverage variation is the difference between the coverage for the head and common ancestor commits of the pull request branch: <coverage of head commit> - <coverage of common ancestor commit>

Diff coverage details

	Coverable lines	Covered lines	Diff coverage
Pull request (#3990)	7	7	100.00%

Diff coverage is the percentage of lines that are covered by tests out of the coverable lines that the pull request added or modified: <covered lines added or modified>/<coverable lines added or modified> * 100%

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