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YAMLtoRefList.pl throws several warnings that don't seem to affect performance

Not sure if this is just on my set up, but maybe it can be cleaned up.
Below warnings are from HopkinsResumeTemplate.tex

mkdir: cannot create directory ‘temp’: File exists
mkdir: cannot create directory ‘output’: File exists
Use of uninitialized value in print at ./perl/YAMLtoRefList.pl line 111.
Use of uninitialized value in print at ./perl/YAMLtoRefList.pl line 114.
Use of uninitialized value in print at ./perl/YAMLtoRefList.pl line 111.
Use of uninitialized value in print at ./perl/YAMLtoRefList.pl line 114.
Use of uninitialized value in print at ./perl/YAMLtoRefList.pl line 111.
Use of uninitialized value in print at ./perl/YAMLtoRefList.pl line 114.
Use of uninitialized value in print at ./perl/YAMLtoRefList.pl line 114.
Use of uninitialized value in print at ./perl/YAMLtoRefList.pl line 114.
Translating temp.tex to temp.html
**** Unknown command \geometry, (0 user-defined) Line 14
**** Unknown parameter/dimension/glue command \parindent = Line 17
**** Unknown parameter/dimension/glue command \columnsep = Line 21
**** Unknown parameter/dimension/glue command \marginparsep = Line 28
**** Unknown command \reversemarginpar, (2 user-defined) Line 29
**** Unknown command \usepackage, (2 user-defined) Line 34
**** Unknown command \hypersetup, (2 user-defined) Line 43
HTML Title constructed as:colorlinks, breaklinks, xetex, bookmarks,
**** Unknown command \pagestyle, (4 user-defined) Line 71
**** Unknown command \fancyhf, (4 user-defined) Line 72
**** Unknown command \fancyhead, (4 user-defined) Line 73
No auxiliary LaTeX file found: temp.aux
**** Unknown parameter/dimension/glue command \extrarowheight = Line 185
**** Unknown or ignored environment: \begin{footnotesize} Line 218
**** Unknown command \clearpage, (6 user-defined) Line 421
Number of lines processed approximately 749

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