gh-39149: Remove executable flags from many Python files
    
For some reason many files are set to be executable. (Presumably some
developer `git clone` sage on some NTFS-based file system or otherwise
don't have proper permissions)

Some of the changes was previously seen in
#38155 or https://github.com/sagema
th/sage/commit/c24e07df70ad46cae0f6a2f58778a90dbb843e05, which has
nothing to do with executable.

On the other hand some files looks like they can rightfully be
executable (because they have the `#!`):
ext_data/pari/dokchitser/testall  and ext_data/nbconvert/postprocess.py
. These files are kept as is.

Moving forward… it might be good idea to have something run on the CI to
check only files with `#!` or PE executable have executable flag.

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### ⌛ Dependencies

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URL: #39149
Reported by: user202729
Reviewer(s):

Author: Release Manager