Updated Readme with rate limit warning + staging URL

There is currently no mention of Let’s Encrypt rate limits or the staging server. I’ve updated the readme so that the rate limit notice is prominently displayed and the necessary config setting to use the staging server is included in the instructions.

changed the way SCRIPTDIR is searched for so it works better with symbolic links (e.g. a symbolic link in ~/.bin)

Added LOCKFILE to config.sh.example

The dns-01 support is now available in production

pass IO descriptors to HOOK transparently

closes #101

See https://twitter.com/letsencrypt/status/689919523164721152

Add hook script example.

Add ability to sign "arbitrary" CSRs

Retain full result when submitting challenge. Fixes #102

Add conf.d support

Fix possibly broken syntax highlighting

Add detail as to how dns-01 hook works

Respect configured BASEDIR for default values

This adds support for a new config variable CONFIG_D in the main configuration
file. Setting a path to a directoy for CONFIG_D advises letsencrypt.sh to
source any additional files found in the specified CONFIG_D directory, that
have a '.sh' ending.
By default CONFIG_D is not set, meaning letsencrypt.sh does not source any
additional configuration files.

If BASEDIR is set in config.sh, this does not modify the (default) values
of either PRIVATE_KEY, WELLKNOWN or LOCKFILE. One needs to manually specify
those three config variables in config.sh, if a different BASEDIR
should be used by letsencrypt.sh.

This commit makes letsencrypt.sh fully aware of a configured BASEDIR.

The pattern
```
 VAR="$(cmd '"')"
```
breaks syntax highlighting in some editors (e.g. gedit or jedit) due to
the tripple double quotes.