[pull] develop from lammps:develop #88
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…orarun/lammps into feature/amber-lammps-bridge
…to to be consistent
- Reorganize content into clear what/how/why structure - Add 'What This Tool Does' section for user understanding - Separate Command Reference (WHAT) from Workflow Examples (WHY) - Organize CLI arguments table by input/output/options - Add comprehensive CLI and Python API examples - Include LAMMPS execution in all workflow examples - Remove duplicate content between sections - Improve RST formatting and consistency - Add AMBER2LAMMPS reference to Tools.rst for discoverability
- Document support for Linux, macOS, and Windows platforms - Specify Windows support via WSL2 or Git Bash - Include Intel and Apple Silicon Mac support - Organize requirements under clear Platform Compatibility section
- Remove placeholder External tools section that was added in previous commit - Restore proper document structure between Pre-processing and Post-processing tools sections
Add AMBER2LAMMPS conversion tool
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