fix(config)!: Correct handling of global_exclude_patterns and directory ignores

Resolves several issues related to the integration and behavior of
`global_exclude_patterns` from `pyproject.toml` configuration and
general directory exclusion logic.

Key fixes and improvements:

1.  **Parameter Passing (`main.py`):** Ensured `config_global_excludes`
    is correctly passed from `flatten_command` to `flatten_code_logic`.
2.  **Directory Exclusion Logic (`ignore_handler.py`):**
    - Modified `is_path_ignored` to correctly exclude files *within*
      a directory matched by a directory pattern (e.g., "docs/"). This
      was achieved by checking if any parent path of a file matches such
      a directory exclusion pattern.
    - Applied this improved parent-checking logic to both config-based
      and CLI-based directory exclusion patterns.
3.  **Test Suite Corrections:**
    - Updated `CliRunner` tests in `test_main.py` to correctly set up
      the `pyproject.toml` within the isolated filesystem used by tests,
      ensuring config is loaded as expected during CLI command invocations.
    - Refined assertions in integration tests to accurately check for the
      presence/absence of specific file headers rather than just string
      content, avoiding false positives from config file content itself.
    - Updated function call signatures in existing tests to accommodate
      the new `config_global_excludes` parameter.
    - Refreshed test snapshots for `tree_generator` to align with the
      corrected ignore/negation logic.

All 101 tests now pass, confirming that `global_exclude_patterns` from
configuration work as intended for both `tree` and `flatten` commands,
and directory exclusion patterns are applied robustly.

BREAKING CHANGE: The behavior of directory exclusion patterns (e.g., "docs/")
is now more comprehensive, ensuring files within such excluded directories are
also ignored. This might alter the output of `tree` and `flatten` for users
relying on the previous, less strict behavior.

Author: Shorzinator