gh-41333: Fix conftest.py being deleted by configure script
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## Problem
When running `make` after switching branches or when reconfiguration is
needed, `conftest.py` (the pytest configuration file) gets deleted.
### Root Cause
The `configure_wrapper` script backs up `conftest.py` before running
`./real_configure` and restores it afterward:
```bash
trap 'mv bak_conftest.py conftest.py; trap - EXIT; exit' EXIT INT HUP
TERM
cp conftest.py bak_conftest.py
./real_configure $@
```
However, when `make` triggers a reconfigure, it runs:
```bash
./config.status --recheck
```
The `config.status` file is generated by `real_configure` and contains a
hardcoded path:
```bash
# Line 502 in config.status
set X /bin/bash './real_configure' $ac_configure_extra_args --no-create
--no-recursion
```
This **bypasses the `./configure` wrapper entirely**, so:
1. `conftest.py` is not backed up
2. `real_configure` runs and deletes all `conftest*` files
3. `conftest.py` is gone
## When This Happens
- Running `make` after `git checkout` to a different branch
- Running `make` after any change that triggers `reconfigure` target
- Running `./config.status --recheck` directly
## Potential Solutions
**Modify `config.status` generation** - Patch the autoconf output to
call `./configure` instead of `./real_configure`
### :memo: Checklist
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- [ ] I have created tests covering the changes.
- [ ] I have updated the documentation and checked the documentation
preview.
### :hourglass: Dependencies
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URL: https://github.com/sagemath/sage/pull/41333
Reported by: Chenxin Zhong
Reviewer(s): Dima Pasechnik, Volker Braun
