Move paths to SampleFileHandler and create get methods for some

[glrs]

This pull request focuses on improving the handling of file paths and directories in the run_sample.py and related files. The most important changes include renaming the base_dir attribute to project_dir, updating method calls to use new helper functions, and ensuring directories are correctly referenced.

Changes to file path handling:

• lib/realms/tenx/run_sample.py: Replaced base_dir with project_dir in pre_process, assemble_cellranger_command, and generate_multi_sample_csv methods. Updated method calls to use new helper functions for CSV paths. [1] [2] [3] [4] [5]
• lib/realms/tenx/tenx_project.py: Added project_dir to project_info dictionary in the __init__ method.

Updates to SampleFileHandler:

• lib/realms/tenx/utils/sample_file_handler.py: Renamed base_dir to project_dir in the class attributes and methods. Added new helper methods get_libraries_csv_path, get_multi_csv_path, and get_feature_reference_csv_path to standardize CSV path retrieval. [1] [2] [3]