The entry point for the e3 IOC shell has been rewritten from being a shell/bash
script to instead be in python. Together with this comes a plethora of changes -
see the CHANGELOG for a more comprehensive description.

Previously, it was the case that running
```
$ iocsh -r module -l cellMods
$ iocsh -l cellMods -r module
```
would both work correctly, but if you looked at the IOC log it was not
clear why that was the case; in the former case it _appeared_ like we
were finding the module before setting `EPICS_DRIVER_PATH`. This only
worked because this variable is exported from the shell.

This change forces the `-l` flag to be processed _before_ all of the
other flags in order to ensure that paths are determined first.

This was needed since we had to have a way for the test suites to override this value. However,
this can also be acheived by writing to configure/CONFIG_CELL.local. This was added in a
refactoring of run_make to make more clear what variables can be passed there.