Updated style sheet and updated paths

`common-definitions.R`, along with other tRNA project related stuff, is
going to be moved to the project directory. In anticipation of this,
paths to some data files have been adjusted.

The colors were updated to the agreed-on colour scheme, and the font was
set.

Fixed a bug regarding the consistent usage of stage names.
Removed the obsolete map function
Vectorisation TODO note added.
Added a `switch` variant for regular expressions
Customised `readable` function

Unify spelling of developmental stages and DOIDs.
Removed some obsolete functions
Removed some obsolete constants
Removed obsolete helpers.R
Removed more obsolete files
Added a concatenator for dictionaries

Concatenate lists with some missing values, replacing missing values by
by those in the first lists where they aren’t missing.
Merge branch 'cdict'