Cleanup `codespell` ignore patterns

[DanielYang59]

Cleanup codespell ignore patterns

Currently a lot of global ignore patterns are very specific to a certain module (or even one line), there's no good reason to ignore a pattern globally for such cases. Admittedly it will be a balance between convenience (no one want to insert a # codespell:ignore tag every line) and correctness (some patterns are very specific to few lines across the code base, but are real typos elsewhere, like lamda/coul, do note).

Changes:

• Keep the global pattern when it's very common: Elements like Nd/Te, or very common for a commonly used module, TITEL for VASP for example, or our good friend atomate
• Rename some internal/test variables when it's not breaking (usually increase readability)
• Ignore all JSON files as comments are not allowed in JSON, we might safely assume everything is intended in JSON

Follow up

• [ ] Is it possible to add file-specific ignore tags (for example ignore ontop for adsorption.py, or coul for LAMMPS)? Currently codespell seems to provide block-level ignore tag but doesn't take a pattern

[DanielYang59]

Thanks! Currently codespell doesn't seem to support block/file level support with pattern, I would update once they do.