Is it only me, or have the insurgencies in Balochistan and KPK increased in intensity by a significant number over the last year or two. While we may say that RAW trains these guys, do not forget the role of the NDS here. Afghan intelligence has been seen providing training and weaponry to the Balochs and the TTP. It is also possible that the logistics pact signed between the BLA and the TTP was mediated by RAW or the NDS. Cooperation between Afghan and Indian intelligence can't be discounted as during the 1970's and 80's, RAW collaborated with KHAD, as Afghan intelligence was known back then, when it came to Pakistani affairs.
Baloch-Pashtun cooperation is not new. In the late 1960's, the Afghan govt's demand for Pakhtoonistan resulted in them funding agitations and militants in KPK, along with encouraging cooperation with the Balochs, as Afghanistan wanted an outlet to the Arabian Sea. After 1971, India also provided aid to Afghan Intelligence along with agents on the ground to foment a movement in KPK and Balochistan. It isn't far-fetched to think the same may be happening now.