Added memory pointers and bitmasks to set master clk
Added defines for pointers
Moved documentation out from src
Updated gitignore
Merge branch 'integration' into pmc

Conflicts:
	.gitignore
	documentation/html/annotated.html
	documentation/html/bug.html
	documentation/html/classes.html
	documentation/html/classpmc.html
	documentation/html/classtest__pmc.html
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	src/test_runner.c
Merge branch 'pmc' into integration