Q1: I get strange errors of inexistent haloes or trees. Why?

A1: Try doing a clean of the post-simulation pipeline,

./project make clean-post-simulation

or of the full pipeline. In principle,

./project make clean-pipeline

should clean out all the files that might be problematic.  Try removing
other temporary built files in the .build/ subdirectories with cosmological
calculations, which in order are:

n-body-init/
haloes/
galaxies/
mergertrees/
voids/


Q2: The .mk files carry out calculations that I think
are unnecessary since they have already been done. Why?

A2: You can understand the exact reasoning used by 'make'
if you add the --debug option to your ./project command,
e.g.

./project make create-galaxies --debug

But best store all output in a log file, e.g.

(./project make create-galaxies --debug 2>&1) | tee mylogfile.1

See also Q1/A1.