feat(#277): Remove Code Duplication Between References

[volodya-lombrozo]

In this PR I combined Linked, Reference and Duplicate classes into a single well-tested class.

Closes: #277.

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PR-Codex overview

The focus of this PR is to refactor code in the opeo package.

Detailed summary

• Removed Linked.java and Reference.java
• Modified StoreArray to handle opcodes differently
• Updated Invocation to handle arguments
• Refactored Constructor to handle different nodes
• Implemented Root to return opcodes
• Updated NewArrayAgent to handle array construction
• Updated tests for ArrayConstructor
• Refactored InvokespecialAgent to handle different nodes
• Updated XmirParser to handle references
• Added tests for Duplicate
• Updated StoreToArrayAgent to handle array storage

The following files were skipped due to too many changes: src/main/java/org/eolang/opeo/ast/Duplicate.java, src/test/java/org/eolang/opeo/decompilation/DecompilerMachineTest.java

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[volodya-lombrozo]

@rultor merge

[rultor]

@rultor merge

@volodya-lombrozo OK, I'll try to merge now. You can check the progress of the merge here

[rultor]

@rultor merge

@volodya-lombrozo Done! FYI, the full log is here (took me 7min)

[0crat]

@volodya-lombrozo Thank you for your contribution! We appreciate your effort, but there are a few areas for improvement. You've earned +5 points: +20 base, -7 for excessive hits-of-code (566 ≥ 200), -15 for missing code review, and -5 for insufficient comments (only 2). We encourage you to focus on quality and ensure proper code review in future submissions. Keep up the good work, and don't hesitate to ask for guidance. Your current balance is +201.