Fixed some formatting issues in Chapter 2

Thanks to @kdavies4 for reporting this.  This closes #207.
Adding a more explicit list of dependencies

This closes #146.
Added ymin for plots and logging of CPU time in results files
Fixed a typo
Trying to create a better example for chattering

This is to address the concerns raised in #205.
Work done in addressing #205

This closes #25.
About to bump up the version to 0.3.6
Fixed a typo