Merged TP2.0/0.9 branch into trunk.
Documentation updates for TP1.3
Minor changes to manual
- No need to escape $ in verbatim environments - sample.conf -> sample_trace.conf
Added new figures
Fixed duplicate label in manual
Updated manual's HTML generation script to better partition the generated HTML.
Minor corrections to manual.
HTML documentation generation script
Wrote missing sections in manual, almost ready for TP1.2
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