Add an alternative Precommit workflow and make pretty

[Growl1234]

This PR introduces a self-contained precommit driver for ABACUS, replacing the previous workflow that relied on GitHub Action built-in/pre-commit style drivers.

The new implementation is inspired by the precommit infrastructure used in CP2K. It provides a project-owned driver under tools/precommit/precommit.py, together with a local precommit server for running external formatting/checking tools in a controlled environment (it would be best if a remote server is configured).

The driver performs strict formatting and file-property checks for files tracked by Git, covering most file types used in the repository. By default, it runs in check-only mode and reports formatting differences without modifying files. When invoked with --allow-modifications, it can automatically fix part of the formatting issues, such as indentation and style inconsistencies.

A convenience script has also been added at the repository root:

./make_pretty.sh

which is equivalent to:

./tools/precommit/precommit.py --allow-modifications

This allows contributors to easily check and fix formatting issues before submitting changes.

This PR also applies make_pretty.sh to the current code base, so most of the diff is purely formatting-related. Also, some tabs and using namespace std; appeared in header codes are fixed based on precommit report.

The new precommit infrastructure is already usable for regular development and CI checks in my view. Some project-specific rules may still require further refinement as more cases are found in practice. I will continue to follow up and adjust the workflow if additional issues are reported.

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[Growl1234]

It also seems some input files are not that pretty now due to my automatic fixes regarding tab characters. Maybe it's worth adding a check regarding ABACUS input files in the future.