@User I migrated over my mag files to a flat directory and magic seems to be confused about paths. It somehow is looking for files with an "_a" appended to them, which I never had, and are not needed in my design. All the modules I use are actually showing up, but it is throwing errors which prevent me from doing extraction.

% load analog_subsystem.mag
File ../modulator/modulator_a.mag couldn't be read
Cell modulator_a is unavailable.  It could not be expanded.
File ../current-sense/current_sense_a.mag couldn't be read
Cell current_sense_a is unavailable.  It could not be expanded.
File ../folded_cascode_p_in/folded_cascode_p_in_a.mag couldn't be read
Cell folded_cascode_p_in_a is unavailable.  It could not be expanded.
File ../bias-circuit/bias_distribution_a.mag couldn't be read
Cell bias_distribution_a is unavailable.  It could not be expanded.
% extract all
Failure to read entire subtree of cell.