Merge in improvements made by Ruth

commit c3d30600220921edcac48167c8a7b0fe794d21b6
Author: Ruth Ivimey-Cook <r.ivimeycook@elifesciences.org>
Date:   Fri Nov 1 17:10:42 2013 +0000

    restart apache in web_app rule now

commit c7b8e7147a811015e76e4691ba77534f90032485
Author: Ruth Ivimey-Cook <r.ivimeycook@elifesciences.org>
Date:   Fri Nov 1 16:32:15 2013 +0000

    comment out phomyadmin,webgrind,xhprof which need config; add vim,curl

commit b56993ab9bb9e624a5661fca52ebf632e000cc01
Author: Ruth Ivimey-Cook <r.ivimeycook@elifesciences.org>
Date:   Tue Oct 29 17:39:03 2013 +0000

    spell include correctly

commit 64f0acdf7bc5160ce12834d62cdcd4a112c0e251
Author: Ruth Ivimey-Cook <r.ivimeycook@elifesciences.org>
Date:   Tue Oct 29 12:46:07 2013 +0000

    rename dev to devtools to clarify purpose

commit 4f1a3a2bfd9af9401a6883eb25e8ff5e6b6a4137
Author: Ruth Ivimey-Cook <r.ivimeycook@elifesciences.org>
Date:   Tue Oct 29 12:44:32 2013 +0000

    rename dev to devtools to clarify purpose

commit 26756f265917feba0059fd2af57849756e958a52
Author: Ruth Ivimey-Cook <r.ivimeycook@elifesciences.org>
Date:   Tue Oct 29 12:43:39 2013 +0000

    clarify and simplify recipes, include xsl and upl_prog as well now

commit 44a82418dd51c2c6583c051aa7d89bc3dddb5ff4
Author: Ruth Ivimey-Cook <r.ivimeycook@elifesciences.org>
Date:   Tue Oct 29 12:43:21 2013 +0000

    clarify and simplify recipes, include xsl and upl_prog as well now

commit 70dae920c6b8d5defb3dc654fc86f8c1972b2464
Author: Ruth Ivimey-Cook <r.ivimeycook@elifesciences.org>
Date:   Mon Oct 28 17:17:02 2013 +0000

    include site_config from the site-specific recipe for the moment. add php mysql module.

commit b6c855a601b1a5a7ccec7ec441e130f08d8fcf9b
Author: Ruth Ivimey-Cook <r.ivimeycook@elifesciences.org>
Date:   Mon Oct 28 12:49:22 2013 +0000

    add version to metadata.rb

commit d1fc01f6cb97181c60538b323fb88658c8cd0f36
Author: Ruth Ivimey-Cook <r.ivimeycook@elifesciences.org>
Date:   Mon Oct 28 12:46:14 2013 +0000

    needed to add attrs for apache

commit 58783baef05d9c5439425158b4a85a2ba6f28f02
Author: Ruth Ivimey-Cook <r.ivimeycook@elifesciences.org>
Date:   Mon Oct 28 12:45:40 2013 +0000

    needed to add depends lines to metadata.rb

commit aa2d050cc626267fc66d0d1bac167a69632b18d8
Author: Ruth Ivimey-Cook <r.ivimeycook@elifesciences.org>
Date:   Fri Oct 25 16:53:02 2013 +0100

    playing with attributes

commit 49d213a6cc634e4ce508d59d90f7490f577d17ef
Author: Ruth Ivimey-Cook <r.ivimeycook@elifesciences.org>
Date:   Fri Oct 25 15:57:39 2013 +0100

    remove commas

commit 6d16950285a6842bf686c3c7b67a4a1b7b3e5eaf
Author: Ruth Ivimey-Cook <r.ivimeycook@elifesciences.org>
Date:   Fri Oct 25 15:35:18 2013 +0100

    revert to using recipes as roles arent found properly

commit d7f62ccd57087d037637329e9cf94a39f3e69697
Author: Ruth Ivimey-Cook <r.ivimeycook@elifesciences.org>
Date:   Thu Oct 24 15:05:58 2013 +0100

    Try to impose some more logic on structure, and document.

commit a6668e43c6dd8e82c37fed0700dc6783d87d7bfa
Author: Ruth Ivimey-Cook <r.ivimeycook@elifesciences.org>
Date:   Wed Oct 23 14:06:21 2013 +0100

    Listen on multiple lines for multiple ports

commit c96200aa18203d3f4f5e5ed9ded5508ca9439939
Author: Ruth Ivimey-Cook <r.ivimeycook@elifesciences.org>
Date:   Wed Oct 23 12:37:04 2013 +0100

    move away from localhost_aliases entirely: use drupal key."

commit b657f2bab8bc3f4f6de2044eaf71d50b632b3c10
Author: Ruth Ivimey-Cook <r.ivimeycook@elifesciences.org>
Date:   Wed Oct 23 12:22:33 2013 +0100

    changes aimed at enabling multiple port apache. Also remove rewrite rules that were messing up some situations.

commit 4ee7d1bc1d776106fb9efbd2a69fff01514f03a8
Author: Ruth Ivimey-Cook <r.ivimeycook@elifesciences.org>
Date:   Tue Oct 22 11:29:58 2013 +0100

    add php5-xsl to get required XSLTProcessor classes

commit 5538bec88d8b40c5e0cc430c7086efefed7b92d9
Author: Ruth Ivimey-Cook <r.ivimeycook@elifesciences.org>
Date:   Fri Oct 18 11:40:16 2013 +0100

    make docroot agree with rest of setup

commit 4bd34c407e4455385bc1c403a83bfb06876b2776
Author: Ruth Ivimey-Cook <r.ivimeycook@elifesciences.org>
Date:   Thu Oct 17 14:41:18 2013 +0100

    mysql hasnt got a minimal recepie