Miscellaneous small issues

[jessecusack]

I am currently reading through the code and will add to this issue with small things as I find them.

Use of true here forces print. Make optional?

perturb/Code/process_VMP_files.m

Line 20 in 0a4928f

my_mk_directory(info.log_filename, true); % Make sure the directory to write logfile to exists

[mousebrains]

Changed to using the already existing debug parameter supplied by get_info or the user.

[mousebrains]

Changed to using the already existing debug parameter supplied by get_info or the user.

[jessecusack]

The point of this issue is to compile miscellaneous small issues rather than creating a new issue every time. I am still reviewing the code and may find more. Reopening.

[jessecusack]

Employ more deliberate printing method?

perturb/Code/mk_filenames.m

Lines 39 to 40 in b69ed0e

	tbl
	rhs

[mousebrains]

This was left over from debugging. It has been removed.