Update write paths in ts_phosim for two use cases:

1) In PhosimCommu.py direct phosim.py to write its output in the chosen output directory. This
a) prevents a problem when the user does not have write access to the phosim_syseng4 directory and
b) allows to run several instances of imgCloseLoop.py simultaneously using the same phosim_syseng installation

2) In CloseLoopTask.py `runWep` https://github.com/lsst-ts/ts_phosim/blob/6413e1d5a1daf18d042f0221b599cb92ab4736da/python/lsst/ts/phosim/CloseLoopTask.py#L799 writes the instName}Pipeline.yaml to the current working directory rather than to the chosen output directory. This means that
a) successive runs of imgCloseLoop.py overwrite the pipeline yaml file and
b) there is no record of the pipeline yaml file that was used to analyse the output stored in a given baseOutputDir