Adding in some formatting of knitr-produced markdown. Styled by pygments. With a print layout that eliminates the left column and the contact info. A good start
Adjusted css for clarity and to center images by default
Convert research and teaching to markdown.
Move javascript to a separate file, adding in the function to move figures to their proper location in the sidebar
Update to test files, and removing html generated by Rstudio
update .gitignore
Merge branch 'master' into knitr_test
Merge branch 'master' into knitr_test

Conflicts:
	.gitignore
	css/default.css
Fixed regression of print style in R docs (this time in the layout, not the css).
Fixed regressions of alignments for R figures & code and format of CV
Merge branches 'staging' and 'master' into knitr_test
Moved setup code & added alignment

Setup code was moved to a single block at the top.
Changed from a  special fig.sidebar to using fig.align with a new option of 'sidebar'
Added alignment classes to the paragraph that contains a figure (or all figures) as specified, using the classes 'align-xxxx'.
updated formatting of R pages, including new style sheet and better handling of printed pages. Contact info moved to the left to ease formatting. (May move it back at some point).
Assign better classes to highlight output.

query code to add more specific classes to highlight classes depending on contents.
This makes for easier formatting of responses separately.
Add generic align-* classes.
convert sidefig.js to new align-* classes

Note that align-* classes are assigned to the paragraph that contains the images (using knitr_jekyll_setup.R as an external source now) so these alignments are done by searching for img tags located within align-* classes. The imgs are not tagged themselves.

Also, added initial code to prevent overlaps. This could probably use refinement to allow figs to shift up as well as down. Not really anxious to write the spring-based layout code or recursive positioning this will need. (It requires thought, at the very least).
No more pretty permalinks

Removed default of pretty permalinks, setting this on a per-file basis. The general plan is to only use pretty links for top-level pages, and leave the more specific pages as standard html. This also simplifies the specification of image/plot locations.
Remove old test files
Also moved shared resources to _knitr directory, which is automatically ignored by Jekyll & easier to reference.
Updates to add an h3 format, and to set max image width
Started adding tutorial files.

Notice format of directory, with _knitr/ directory to hold the source files.

Build source files using knitr, from the directory *above*  the _knitr directory.