For those looking for multiple staging areas in Git, git-cl provides this functionality.
Instead of repeatedly cycling through git add -p, you can organise changes by intent at the file level:
git cl add bugfixes solver.py utils.py # Bug fixes
git cl add features analysis.py plotting.py # New features
git cl status # See organised changes
git cl commit bugfixes -m "Fix convergence issues"
For scenarios involving many smaller commits from a large changeset, you can organise changes as you work (git cl add hotfix equations.py) then commit each logical group when ready. This solves the multiple staging area problem while working with Git's existing staging model