gh-38816: fix all pep E302 in manifolds and geometry
this is about fixing the warning
E302 expected 2 blank lines, found 1
in the `manifolds` and `geometry` folders.
Purely scripted using `autopep8`
### :memo: Checklist
- [x] The title is concise and informative.
- [x] The description explains in detail what this PR is about.
- [ ] I have linked a relevant issue or discussion.
- [ ] I have created tests covering the changes.
- [ ] I have updated the documentation and checked the documentation
preview.
URL: https://github.com/sagemath/sage/pull/38816
Reported by: Frédéric Chapoton
Reviewer(s): Vincent Macri
