Bug in collect plausible patches script

[islem-esi]

The current implementation of plausible patches collection only gets mutation-based plausibles...

[JYe9]

Hi @islem-esi Thanks for maintaining this amazing project. I've reproduced and analyzed the bug in collect_plausible_patches_files.py and would like to share my findings.

Reproduction Steps (using dev container):

mkdir -p experimental_setups/test_batch
echo "Closure 65" > experimental_setups/test_batch/test
./run_on_defects4j.sh experimental_setups/test_batch/test hyperparams.json
python3.10 experimental_setups/collect_plausible_patches_files.py 18 19

Root Cause Analysis:

1. The agent only stores mutation-based patches in plausible_patches/ when all tests pass (agent.py#L278-L280):

   with open(os.path.join("experimental_setups", exps[-1], "plausible_patches", ...), "a+") as exps:
       exps.write("### PLAUSIBLE FIX\\n{}\\n".format(str(m)))
   

2. The collection script only checks one directory (collect_plausible_patches_files.py#L?):

   if os.path.exists(os.path.join("experiment_{}".format(i), "plausible_patches")):
       patches[i] = patches[i] + os.listdir(...)
   

Proposed Solutions:

1. Extend collection script to check additional directories
2. Consolidate storage - make all patch types save to plausible_patches/
3. Add configurable parameters for patch sources

I'm happy to submit a PR with the fix once we decide on the solution direction.