sage_setup: Modify clean_stale_files to support out-of-tree namespace packages

[mkoeppe]

Follow-up from #28925.

We modify clean_stale_files so that the incremental install logic of sagelib can work even if we want to install namespace packages in addition to sagelib, such as:

• sage.numerical.backends.coin_backend. The package sage.numerical.backends is turned into a namespace package. It serves as an example of a module in a namespace package that is maintained outside of the sage source tree (here: https://github.com/mkoeppe/sage-numerical-backends-namespace)

Depends on #32874

Component: refactoring

Branch/Commit: u/mkoeppe/out_of_tree_namespace @ d825e55

Reviewer: Kwankyu Lee

Issue created by migration from https://trac.sagemath.org/ticket/30152

[mkoeppe]

Dependencies: #28925

[mkoeppe]

Branch: u/mkoeppe/out_of_tree_namespace

[mkoeppe]

comment:3

Setting new milestone based on a cursory review of ticket status, priority, and last modification date.

[mkoeppe]

comment:8

Not needed with #32874

---

New commits:

ef4e554	Merge branch 't/30277/remove_src_module_list_py' into t/28925/modify_find_python_sources__clean_stale_files_to_support_modularization_of_sagelib_by_native_namespace_packages__pep_420_
6282b8d	sage.graphs.graph_decompositions: Make it a namespace package by removing __init__.py (which had unnecessary reimports only)
7c10680	sage.numerical.backends: Make it a namespace package by removing __init__.py (which was empty)
6e68259	Mark src and src/sage/ext_data as directories that are not namespace packages
b71c3a6	sage_setup.find.find_python_sources: Handle native namespace packages, 'nonamespace' files
3a12146	is_package_or_namespace_package_dir: New, recognize namespace packages by file 'namespace', monkeypatch into Cython
98a1b88	sage_setup.command.sage_install.sage_install: Rename to sage_install_and_clean, update use it in src/setup.py; refactor through new class sage_install
6892432	sage_setup/command/sage_install.py: WIP: Disable cleaning
b6e771d	Revert "sage_setup/command/sage_install.py: WIP: Disable cleaning"
d825e55	WIP

[mkoeppe]

Changed dependencies from #28925 to #32874

[mkoeppe]

Commit: d825e55

[kwankyu]

Reviewer: Kwankyu Lee

[kwankyu]

comment:9

Okay. See #32927 comment:36