Reorganize the tools folder

[mohanchen]

…alysis script

This commit consolidates three previous commits (#1, #2, #3) into a single comprehensive refactor of the tools/ directory, addressing both organizational structure and a path-related bug in the code analysis script.

1. tools/ directory reorganization

   • Group all numerical atomic orbital (NAO) generation tools under 01_NAO_generation/, including: * SIAB/ (Simulated Annealing method in C++) * pytorch/ and pytorch_dpsi/ (PyTorch gradient methods) * pytorch_gradient_source/ (original PyTorch implementation) * lcao_bash/ and abfs_bash/ (bash-based orbital generators) * qo/ (quasiatomic orbital generation) * Generate_Orbital_AllInOne.sh (main entry script) * examples/ (example input files)
   • Move all post-processing and visualization tools under 02_postprocessing/:
     • rt-tddft-tools/, stm/, average_pot/, selective_dynamics/, plot-tools/
   • Place source code analysis tools under 03_code_analysis/
   • Rename windows/ to 04_windows_installation/ for consistency
   • Use numerical prefixes (01_, 02_, 03_, 04_) to define a clear order
   • Use git mv to preserve file history throughout the refactor

2. New tools/README.md

   • Add a comprehensive README with directory tree, quick start guide and tool descriptions

3. Fix generate_include_analysis.py path bug

   • The script computed repo_root using os.path.dirname(script_dir), assuming the script lived in tools/. After moving to tools/03_code_analysis/, this resolved to tools/ instead of the repository root, causing os.walk to find no source files.
   • Update to os.path.dirname(os.path.dirname(script_dir)) to correctly resolve the repository root from the new script location.

Combined previous commits:
6e3b7954c add code analysis python file
546d7cd76 update tools
92094b81d update

Reminder

• Have you linked an issue with this pull request?
• Have you added adequate unit tests and/or case tests for your pull request?
• Have you noticed possible changes of behavior below or in the linked issue?
• Have you explained the changes of codes in core modules of ESolver, HSolver, ElecState, Hamilt, Operator or Psi? (ignore if not applicable)

Linked Issue

Fix #...

Unit Tests and/or Case Tests for my changes

• A unit test is added for each new feature or bug fix.

What's changed?

• Example: My changes might affect the performance of the application under certain conditions, and I have tested the impact on various scenarios...

Any changes of core modules? (ignore if not applicable)

• Example: I have added a new virtual function in the esolver base class in order to ...

[Critsium-xy]

This PR has one major problem: the pathes of file in some docs and files are not changed.

For example:

1. docs/advanced/windows_installer.md
2. source/source_io/module_qo/to_qo_kernel.cpp:417
3. source/source_basis/module_nao/atomic_radials.cpp:117-118, 287-288 (Not important)

No other problems exist.