Some abilities have a [Click] cost to them, such as Crypsis' ability to add a virus counter to it.
Does it count as a "paid ability" for the purposes of the Run Timeline? I.e. could I, mid-run, add a virus counter to Crypsis for the cost of one [Click]?
No. If an ability has a [Click] as part of its cost, it can only be used as a main action in the controlling player's turn. It cannot be used on the other player's turn or during a run.
From the rules (PDF) page 21, under Paid Abilities (emphasis mine):
Paid abilities can be triggered at the beginning of each turn, before and after each player action, and at certain points during a run, unless the ability requires a click, in which case it must be triggered as an action.
No, the rules state that abilities with a Click cost can only be used as an action. So since a run is an action you must wait for the run to finish before activating Crypsis. (Or use it before the run.)
No. Any abilities that cost a click are actions, and actions can only be used in that players action phase, and that action must be fully resolved before another action can be used.
There are some cards where clicks are still spent during a run. The most notable card which is printed with a click costed ability is Adjusted Matrix, which modded an icebreaker into an AI with:
[Click]: Break Ice Subroutine.
This ability has been errataed to:
You may spend [Click] to break any subroutine on a piece of ice currently being encountered.
To prevent this confusion. This is the same wording as used on bioroids, such as Eli 1.0, which are the most common exception to not spending clicks outside of the action phase.
