Bf/startup

This fixes two issues

1. Using the system activate may fail as it can start using the conda libraries in FSLDIR which may not be compatible, e.g.:

  File "/opt/fmrib/conda/python3/bin/conda", line 12, in <module>
    from conda.cli import main
  File "/vols/Scratch/mwebster/fsl_dafc4c0c/lib/python3.12/site-packages/conda/cli/__init__.py", line 3, in <modul
e>
    from .main import main  # NOQA
  File "/vols/Scratch/mwebster/fsl_dafc4c0c/lib/python3.12/site-packages/conda/cli/main.py", line 6, in <module>
    from ..deprecations import deprecated
  File "/vols/Scratch/mwebster/fsl_dafc4c0c/lib/python3.12/site-packages/conda/deprecations.py", line 60
    if version_tuple := self._get_version_tuple(version):

2. The current script will try to build in the test directory and not the output directory. This fix simply copies the Makefile and source files to the output directory.