Update dependencies

[breznak]

Update most dependencies to the latest versions:

• capnp (we missed that during Update capnp #1302 )
• yaml
• yaml-cpp WIP ..currently fails, => moved to Upgrade to new YAML-cpp API (old v0.3.0 holds back yaml, yaml-cpp)  #1319
• boost headers to 1.64.0
• swig to 3.0.12, replaces Update to latest swig version (3.0.12 as of 5/10/2017) #1292

Fixes #1308
Fixes #1293

[breznak]

Commit 30def6c updating yaml-cpp is known to fail, I'll have to revert it. We are using the old API version 0.3.0, while upstream is it 0.5.3 - would it be possible for us to easily transition?
Otherwise this PR passes OK locally, so the rest of the commits are ready for review/merge.

@oxtopus @vitaly-krugl

[breznak]

Windows swig build fails
https://ci.appveyor.com/project/numenta-ci/nupic-core/build/0.3.0.2101/job/4h33kp4iamn7nt4h#L1289
is it related to the expected) #1292 (review) (part 1, win)? Or another issue? If the former, we can try to install the special win binary as suggested
http://prdownloads.sourceforge.net/swig/swigwin-3.0.12.zip

[vitaly-krugl]

Commit 30def6c updating yaml-cpp is known to fail, I'll have to revert it. We are using the old API version 0.3.0, while upstream is it 0.5.3 - would it be possible for us to easily transition?
Otherwise this PR passes OK locally, so the rest of the commits are ready for review/merge.

@breznak, I have not had the opportunity/time to look into the new Yaml-cpp API, so can't comment on how easily we might transition to it.

[vitaly-krugl]

Windows swig build fails
https://ci.appveyor.com/project/numenta-ci/nupic-core/build/0.3.0.2101/job/4h33kp4iamn7nt4h#L1289
is it related to the expected) #1292 (review) (part 1, win)? Or another issue? If the former, we can try to install the special win binary as suggested
http://prdownloads.sourceforge.net/swig/swigwin-3.0.12.zip

cc @scottpurdy

@breznak, it would be reasonable to follow SWIG's recommendation per @scottpurdy's review feedback. That said, this pull request might be attempting too many things. Perhaps SWIG upgrade could be done via a separate PR out of practical considerations.

[breznak]

Closing as suggested, will provide smaller, separate PRs instead.