project_dir is hardcoded and is sometimes "./" and sometimes "../"; this should be a conf file settings

[mmaiers-nmdp]

create a new configuration parameter for the "working directory" (e.g. "working_dir")

use this throughout in place of project_dir
make the default "." for portability

[mmaiers-nmdp]

for example imputation_in_file is pre-pended with "./" which doesn't work when absolute paths are used.