do not force the permalink to be a dir if it ends on .html

Fixes #798.
test per-post permalinks

Add tests for setting a permalink on a post (in YAML frontmatter),
both the "old way" (generating an index.html) and with an .html ex-
tension.
use binary mode when writing file.
Only generate excerpts if the excerpt_separator isn't blank
We don't need excerpts in jekyllrb.com
bugs in the site
Just clarifying the Post#should_generate_excerpt?
Docs about disabling excerpts.
Cleaned up the deprecator a little
Print warning when `paginate` is set to `true`.

Related to #1105.

Sample output:
~/code/jekyll/tsite$ ../bin/jekyll build --trace
Configuration file: /Users/parker/code/jekyll/tsite/_config.yml
    Config Warning: The `paginate` key must be a positive integer or nil. It's currently set to 'true'.
            Source: /Users/parker/code/jekyll/tsite
       Destination: /Users/parker/code/jekyll/tsite/_site
      Generating... done.
paginate option cannot be 0.
Add test for Configuration#fix_common_issues
Use .empty? instead of == ''
Merge pull request #1364 from koron/write-in-binary-mode

use binary mode when writing file.
Update history to reflect merge of #1364
Add -D short-form switch for drafts

Add -D short-form switch for the drafts option, to compliment --drafts
Merge pull request #1394 from catsby/drafts_flag

Add -D short-form switch for drafts
Update history to reflect merge of #1394
Merge pull request #1390 from mojombo/better-errors

Catch and fix (somehow) common configuration errors
Update history to reflect merge of #1390