Move paths to SampleFileHandler

[glrs]

This pull request focuses on refactoring the handling of directory paths in the SS3Sample class and related methods, moving the responsibility to the SampleFileHandler class. The most important changes include renaming base_dir to project_dir, removing the project_dir and sample_dir attributes from SS3Sample and updating methods to use SampleFileHandler for directory paths.

Refactoring directory path handling:

• lib/realms/smartseq3/ss3_sample.py: Removed project_dir and sample_dir attributes from SS3Sample and updated methods to use SampleFileHandler for directory paths. [1] [2] [3] [4]
• lib/realms/smartseq3/utils/sample_file_handler.py: Updated SampleFileHandler to initialize project_dir and sample_dir based on sample.project_info and refactored methods to use these attributes. [1] [2]