People here are assuming that the Spurs want to swallow that $4m contract from Bonner through the amnesty... I don't think that's the case at all.
At some point the Spurs had to decide whether to throw $1m in the trash in order to get capspace or guarantee the $4m deal and turn it into a tradeable contract, and it's obvious they decided the later. From there on out, the rest was fairly predictable: re-sign your own talent, replace Blair and potentially Neal, and see if you can use that $4m chip + some other smaller contracts to flip into some usable talent (ie: AK).
The FO didn't even need to ask Manu for a $2m discount. They could've simply structured his deal as a 3 season deal, with only $3m guaranteed in the 3rd year and a team option. But IMO, it's pretty clear that using capspace wasn't the plan at all.