bpo-45886: Fix OOT build when srcdir has frozen module headers (GH-29793)

bpo-45886: Fix OOT build when srcdir has frozen module headers (GH-29793)

The presence of frozen module headers in srcdir interfers with OOT
build. Make considers headers in srcdir up to date, but later builds do
not use VPATH to locate files. make clean now removes the headers, too.

Also remove stale ``_bootstrap_python`` from .gitignore.