Refactor PhyloDiscrete simulator framework

[Ming11110]

Key Changes

phylonco-lphy:

1. CopyNumberBD.java

   • Added comprehensive documentation with usage examples.
   • Support flexible parameterization: single bdRate or separate lambda/mu (prepared for future flexibility).
   • Made nstate parameterizable with default value of 15.

2. PhyloDiscrete.java

   • Removed unnecessary realData parameter.
   • Simplified class structure.

3. IntegerCharacterMatrix.java

   • Code cleanup and improved organization.

4. ReadCopyProfile.java

   • Added usage example: "CopyNumber_Yule.lphy".

5. CopyNumberModelTest.java

   • Comprehensive test coverage for both parameterization modes.
   • Test bdRate mode (current implementation).
   • Test lambda/mu mode (future-ready).

phylonco-lphybeast:

1. PhyloDiscreteToBEAST.java

   • Updated to match PhyloDiscrete refactoring.

2. CopyNumberBDToBEAST.java

   • Properly retrieve nstate parameter instead of using hardcoded default.

3. IntegerCharacterMatrixToBEAST.java

   • Calculate totalcount (maximum copy number) from actual data.