Merge pull request #3 from ewels/gh-pages

Help with the new SAMTools website
set the site.baseurl in the jekyll config
fixed "Get source release" link on the homepage
added CRAM workflow text and new section
added link to CRAM workflow
added link to CRAM workflow
minor text formatting edits to CRAM section
fix for workflows dropdown where the list had a syntax error
minor text formatting edits to CRAM section
added link at top of the page to the different workflows
fixed syntax for link at top of the page to the different workflows
rewording of sentence suggested by James B.
Adds Dockerfile for site testing and development
Update links for 1.1 release
Merge Dockerfile addition (PR #2)

Also exclude Dockerfile and rename docker/ to an _-prefixed directory
to prevent Jekyll from copying these files to _site/.
Fix publication links
Add manpage layout template

Move <head>,</head> tags from _includes/head.html to the layout so
that the layout can add extra things to <head>.  Reformat templates
to minimise excess blank lines and borken indentation.
Add manual pages to the web site

Both bcftools-1.x.html files were generated via bcftools's make rule
from the respective tags.  docbook-xsl.css was produced as a byproduct
and is constant across versions.

samtools-1.1.html was generated from samtools's 59c56f0;
samtools-1.0.html was generated by applying that as a patch to faf4dd6;
samtools-0.1.19.html was generated by similarly patching the 0.1.19 tag.

tabix-1.1.html was generated from htslib's a0e35e0; tabix-1.0.html was
generated by applying that as a patch to the 1.0 tag.  In 1.1 and before,
bgzip is documented within tabix.1 rather than having a separate man page.

faidx.html, sam.html, and vcf.html were generated from htslib's 1.1 tag,
and are not versioned as they change only infrequently and compatibly.

Versioning the man page links partially addresses samtools/bcftools#115.

Fixes #5: for bcftools, the native a2x output does not use en dashes;
for samtools and tabix, the source no longer (ab)uses \- for options.
Resolved merge conflicts
Merge branch 'samtools-gh-pages' into gh-pages