It would be great to...
be able to specify library/search paths.
This is necessary for include files that are outside of the project.

It is now possible to add an --include command line option so that LilyPond can 
find these files, but elysium doesn't know about them.
As a result the user gets wrong warnings (about unknown variables), 
and elysium/eclipse can't use these references for code navigation and other 
tricks.

Suggestion:
Add a multi-line field in Preferences->LilyPond->Compiler where one can enter 
multiple folders as LilyPond include paths (should be selectable by a file 
dialog).
These folders should then automatically be used as additional command line 
parameters for the lilypond command (this should be an addition to and not a 
replacement of the other quite new feature for additional parameters).

It should then be made possible that elysium searches these directories for 
variable declarations (in validation and code navigation).
Attention: LilyPond also uses subdirectories for this:
If I do --include=~/folder/foo and then write 
\include "tweaks/test.ily" 
into my source file, lilypond also finds the file ~/folder/foo/tweaks/test.ily

I hope this doesn't conflict with eclipse's Workspace policy.
If the second part of the enhancement isn't (easily) possible to achieve, the 
first part would already make a useful enhancement.