Proof Management: Ignore internal contracts when calculating dependency state (fixes #3745)

[WolframPfeifer]

This PR fixes an issue with calculation of dependencies: Dependencies to contracts that are not in user-provided sources (e.g., in bootclasspath) are not reported as unproven dependencies any more. However, they are still shown in the "Dependencies" tab in the report, and are still printed on the console with INFO log level.

Related Issue

This pull request resolves #3745.

Type of pull request

• Bug fix (non-breaking change which fixes an issue)
• There are changes to the (Java) code

Ensuring quality

• I made sure that introduced/changed code is well documented (javadoc and inline comments).
• I have tested the feature as follows: Manually with the example provided in Proof management report claims proofs for JavaRedux methods are missing #3745 and a similar one.

Additional information and contact(s)

The contributions within this pull request are licensed under GPLv2 (only) for inclusion in KeY.