phases: do not reanalyze amodules in run_phase

Multiple `run_phase` invocation should not analyze a amodule twice.

This is a workaround, the whole phase API should be improved to make late
module loading less error-prone and more simple.

Close #726 
Ca attendra la meilleure api je pense. je veux pas trop que les gens commencent a lire dedans, surtout si ca change.