[cleanup] Move non-sys and non-ref colors out from theme-colors.css

This moves all non-sys and non-ref definitions from theme-colors to
application-color-tokens.

Bug: 390330089
Change-Id: Ia3b667a72b5ed02bcddf4d89adfd820c69299a64
Reviewed-on: https://chromium-review.googlesource.com/c/devtools/devtools-frontend/+/6197649
Commit-Queue: Benedikt Meurer <[email protected]>
Auto-Submit: Kim-Anh Tran <[email protected]>
Reviewed-by: Benedikt Meurer <[email protected]>
Commit-Queue: Kim-Anh Tran <[email protected]>

Author: ktran