Fix bugs and improve code organization across SimiCPipeline

[Copilot]

Several correctness bugs, API hygiene issues, and code organization problems existed across the package. This PR addresses them with surgical, targeted changes.

Bug Fixes

• @staticmethod on module-level function (utils/io.py): format_time was decorated with @staticmethod at module scope, producing a staticmethod descriptor object instead of a callable — any call would raise TypeError.
• __all__ typo (simicpipeline/__init__.py): "AUProcessor" was appended instead of "AUCProcessor", so the class was silently missing from the public API.
• == None identity check (utils/io.py): adata.raw == None → adata.raw is None.
• load_from_matrix_market path handling: genes_path/cells_path typed as Union[str, Path] with None defaults but .exists() called directly on them. Fixed type hints to Optional[Union[str, Path]] with explicit is not None guard and Path(...) conversion.

API / Public Surface

• Renamed install_package → _install_package and removed it from utils/__init__.py exports. A library package should not expose a pip-installer as public API.
• Removed setup.cfg — fully redundant with pyproject.toml; settings conflicted (mypy Python 3.9 vs 3.10, line length 100 vs 88).

Dead Code & Import Cleanup

• Removed large blocks of commented-out class definitions in core/__init__.py, aucprocessor.py, simicpreprocess.py.
• Removed unused imports (os in _jupyter.py; numpy, coo_matrix, Tuple in utils/io.py).
• Removed stale section-separator comments; fixed misindented comment inside print_tree docstring.

Tests

Added tests/ directory (previously missing despite pytest being configured) with 14 smoke tests covering format_time, write_pickle, print_tree, SimiCBase, and _load_assignment_file.