JCas cover annotation created in PEAR context replaced during index operations

Initial title: MARKFAST don't work when a Ruta 3 script runs in an AAE inside a PEAR context

When an AAE runs in a PEAR context, and the first analysis engine is a Ruta script with MARFAST (or MARKTABLE) actions, those actions don't work (same situation after a CAS multiplier).

The problem seems to be coming from RutaStream#moveToFirst when it's called from TreeWordList.find; in that case, the underlying iterator is not properly reset. It may be something related with the RutaStream "bootstrapping"... I don't know

If a new Ruta script (for instance, an empty script) is placed before the "problematic" one, the problem with those MARKFAST/TABLE actions goes away. 

Example here: https://github.com/benisantos/ruta3-markfast-pear-bug

Note: with UIMA/Ruta 2.x this problem doesn't exist at all.