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cleanup (#1301)

* BFB cleanup stuff

* Adding some helper routines

* More BFB changes

* More BFB changes

* More BFB changes

* More BFB changes

* Fixing python API and adding an agent file and a prompt to fix python API in the future.

* Updating scripts and improving formatting

* Updating some scripts and adding new jenkins test to compare the current branch vs master with flags

* Restoring BFBness when using l_lmm_stepping=.true. by reimplementing an existing bug...

* Making run_clubb_w_varying_flags.py not remove output, it's just unneccesary

* Simplifying script changes

* Jenkins script update

* Little consolidation of code in pdf_closure_driver

* Fixing python API

* Fixing parameterization_check formatting
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