The character generator now stays with your agent beyond creation. Open it from My agents or from the finished file with Advancement.
After the mission you enter the XP: file colour, objective, personal bonus and threads found, exactly by the current rules. Rank counts all XP ever received.
During downtime you spend it. Skills, class tree nodes, psi powers and spells are available at once. A new skill needs a teacher, an attribute takes the whole downtime. The generator checks rank, prerequisites and maximums and can undo every step.
The character sheet then shows rank, XP, your own branch with every node acquired and the career log. The exported file carries the advancement over to Foundry VTT (version 0.8.1 or later).