Improve docs, get tests working in CI, and consolidate file I/O implementation

[zanebeckwith]

This PR:

• Streamlines the Bash scripts somewhat, to make it easier to test the library (especially with TPM support when testing against a simulator)

• Makes a trivial change to our usage of the AMCL API, which will make it easier to use newer versions of that library (also fixed a trivial issue that was upsetting static analysis tools)

• Removes a (unneeded) test that was upsetting Memcheck

  • A full justification of this removal can be found in the commit message for commit 9f0e47d

• Gets all tests working (and passing) in Travis-CI again, and fixes numerous issues with those that had arisen

  • This includes making a few trivial changes to satisfy static analysis tools (the justification of these can be found in the commit messages)

• Restructures the file I/O logic, in order to perform better error checking

  • This was in response to complaints from Coverity Scan static analysis tool

• Significantly reorganizes and augments the documentation

95% of this work I did back in the summer, then got busy and let it sit. I'm polishing it off (just finishing some documentation updates) now and getting it submitted.

fixes #90 fixes #110 fixes #122 fixes #123

[coveralls]

Coverage decreased (-0.2%) to 83.639% when pulling 3530839696caaef7558a3ade69169c5ed90053b1 on zanebeckwith:improve-docs into 27444ef7166f62fff819a5c9563a495d954fcd8e on xaptum:master.

[zanebeckwith]

Yea, good call on changing the threshold for the Coveralls check. All the "template" expansion shenanigans in this build have, for some reason, always totally confounded Coveralls, so pretty much every trivial PR causes some fractional shift in the coverage.

I bumped the threshold to -2% for a failure