Branch "bleeding-edge" of refbase code from SourceForge

* https://sourceforge.net/p/refbase/code/HEAD/tree/branches/bleeding-edge/
* svn checkout https://svn.code.sf.net/p/refbase/code/branches/bleeding-edge

AUTHORS

+This file lists current & previous members of the refbase development team
+and other contributors.
+
+Please avoid sending e-mail with refbase-related questions directly to them;
+your questions are likely to be answered much faster if you post them to one
+of the mailing lists or forums:
+  <http://support.refbase.net/>
+
+msteffens:Matthias Steffens <refbase@extracts.de>:
+ Project manager, lead developer, application engineering & design
+
+karnesky:Richard Karnesky <karnesky@gmail.com>:
+ Project manager, application engineering, MODS XML export, Endnote style,
+ COinS, update.php, some bugfixes & docs
+
+pnault:Pierre Nault <pnault@users.sourceforge.net>:
+ Localization efforts, some bugfixes
+
+Previous developers:
+
+Michael Bartz <michaelbartz@users.sourceforge.net>:
+ Advisor
+
+wendebaum:Jochen Wendebaum <wendebaum@users.sourceforge.net>:
+ Internationalization, german localization
+
+Daniel Stepputtis <antedon@users.sourceforge.net>:
+ Documentation & general support
+
+Thanks to:
+
+- Joachim Almergren <jlacan@users.sourceforge.net>:
+  Various patches
+
+- Oleksandr Moskalenko <oleksa@users.sourceforge.net>:
+  Troubleshooting and patch for directory renaming
+
+- Dave Burt:
+  Fix for MODS encoding
+
+- Nicholaus Lance Hepler <nhelper@gmail.com>:
+  Patch to retrieve information from PubMed before CrossRef
+
+- Yibiao Bai <mountangellib@gmail.com> and Yong Fan, Shanxi Agricultural
+  University Library, China:
+  Chinese localization.
+
+- Alexander Belozerov <alexander.belozerov@gmail.com>:
+  Russian localization.
+
+- Masahiro Mikami <ZBN15427@nifty.com>:
+  Japanese localization.
+
+- Chris Putnam <cdputnam@scripps.edu>:
+  Developer of Bibutils, a set of command line programs that interconvert
+  between various bibliography formats using a common XML intermediate.
+  <http://www.scripps.edu/~cdputnam/software/bibutils/bibutils.html>
+
+- Mark Grimshaw <sirfragalot@users.sourceforge.net>:
+  Developer of MINIMALRTF, a minimal set of RTF coding methods to produce
+  Rich Text Format documents on the fly. <http://bibliophile.sourceforge.net>
+
+- Wayne Munro at R&OS New Zealand:
+  Developer of the module-free pdf-PHP class that allows to dynamically create
+  PDF documents with PHP. <http://www.ros.co.nz/pdf>
+
+- Ryan Parman and Geoffrey Sneddon:
+  Developers of the SimplePie PHP class that allows to manage RSS and Atom feeds
+  with PHP. <http://simplepie.org>
+
+- Thomas Fuchs and contributors:
+  Developers of the script.aculo.us JavaScript framework. <http://script.aculo.us>
+
+- Sam Stephenson and contributors:
+  Developers of the Prototype JavaScript framework. <http://www.prototypejs.org/>
+
+- nijel and garvinhicking of the phpMyAdmin project:
+  Developers of zip.inc.php, which is used to zip OpenDocument files.
+  <http://www.phpmyadmin.net>
+
+- Ryan Thrash:
+  Developer of the "Simple Rounded Corner CSS Boxes".
+  <http://www.modxcms.com/simple-rounded-corner-css-boxes.html>
+  see also the ThrashBox online generator at <http://www.spiffybox.com/>
+
+- Hugh E. Williams and David Lane, authors of the book "Web Database Applications
+  with PHP and MySQL", published by O'Reilly & Associates, whose example code
+  helped getting started. <http://www.oreilly.com/catalog/webdbapps2/>
+
+Many other people have contributed to this project with feature requests, bug
+reports, testing, and helpful suggestions.

BUGS

+We are aware of the following problems, bugs and/or limitations:
+
+- The clickable search links do not maintain the current sort order,
+  and they do not maintain the currently chosen fields in List view.
+
+- For the main page, only partial HTML is returned when clicking one of the
+  clickable search links within the "more info" section underneath each
+  citation.
+
+- The advanced search form employs lots of dynamic drop-down menus to ease
+  user entry of data. This works well for small databases (<10,000 records)
+  but may cause significant speed problems for larger databases!
+
+- There's no support for transactions. This means that multiple users will be
+  able to edit the same record at the same time. This will usually cause the
+  record to be overwritten by the last submitter, but it could cause
+  surprising results. Please remember to reload record data if you kept a
+  record's "edit" form open for a long period of time.
+
+- The 'allow_edit_call_number' permission setting isn't honoured yet.
+
+- The process of internationalization and localization has not been completed
+  yet.
+
+- Working simultaneously in different browser windows or tabs may cause some
+  unexpected results (due to referrer-related issues). You can avoid problems
+  if you reload the current browser window/tab before doing anything else in
+  that window/tab.
+

COPYING

+		    GNU GENERAL PUBLIC LICENSE
+		       Version 2, June 1991
+
+ Copyright (C) 1989, 1991 Free Software Foundation, Inc.
+     59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
+ Everyone is permitted to copy and distribute verbatim copies
+ of this license document, but changing it is not allowed.
+
+			    Preamble
+
+  The licenses for most software are designed to take away your
+freedom to share and change it.  By contrast, the GNU General Public
+License is intended to guarantee your freedom to share and change free
+software--to make sure the software is free for all its users.  This
+General Public License applies to most of the Free Software
+Foundation's software and to any other program whose authors commit to
+using it.  (Some other Free Software Foundation software is covered by
+the GNU Library General Public License instead.)  You can apply it to
+your programs, too.
+
+  When we speak of free software, we are referring to freedom, not
+price.  Our General Public Licenses are designed to make sure that you
+have the freedom to distribute copies of free software (and charge for
+this service if you wish), that you receive source code or can get it
+if you want it, that you can change the software or use pieces of it
+in new free programs; and that you know you can do these things.
+
+  To protect your rights, we need to make restrictions that forbid
+anyone to deny you these rights or to ask you to surrender the rights.
+These restrictions translate to certain responsibilities for you if you
+distribute copies of the software, or if you modify it.
+
+  For example, if you distribute copies of such a program, whether
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+
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+(2) offer you this license which gives you legal permission to copy,
+distribute and/or modify the software.
+
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+that everyone understands that there is no warranty for this free
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+want its recipients to know that what they have is not the original, so
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+  Finally, any free program is threatened constantly by software
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+  The precise terms and conditions for copying, distribution and
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+
+		    GNU GENERAL PUBLIC LICENSE
+   TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND MODIFICATION
+
+  0. This License applies to any program or other work which contains
+a notice placed by the copyright holder saying it may be distributed
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+
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+
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+
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+
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+
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+certain countries either by patents or by copyrighted interfaces, the
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+
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+Software Foundation.  If the Program does not specify a version number of
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+Foundation.
+
+  10. If you wish to incorporate parts of the Program into other free
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+
+			    NO WARRANTY
+
+  11. BECAUSE THE PROGRAM IS LICENSED FREE OF CHARGE, THERE IS NO WARRANTY
+FOR THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW.  EXCEPT WHEN
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+
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+PROGRAMS), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE
+POSSIBILITY OF SUCH DAMAGES.
+
+		     END OF TERMS AND CONDITIONS
+
+	    How to Apply These Terms to Your New Programs
+
+  If you develop a new program, and you want it to be of the greatest
+possible use to the public, the best way to achieve this is to make it
+free software which everyone can redistribute and change under these terms.
+
+  To do so, attach the following notices to the program.  It is safest
+to attach them to the start of each source file to most effectively
+convey the exclusion of warranty; and each file should have at least
+the "copyright" line and a pointer to where the full notice is found.
+
+    <one line to give the program's name and a brief idea of what it does.>
+    Copyright (C) <year>  <name of author>
+
+    This program is free software; you can redistribute it and/or modify
+    it under the terms of the GNU General Public License as published by
+    the Free Software Foundation; either version 2 of the License, or
+    (at your option) any later version.
+
+    This program is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+    GNU General Public License for more details.
+
+    You should have received a copy of the GNU General Public License
+    along with this program; if not, write to the Free Software
+    Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
+
+
+Also add information on how to contact you by electronic and paper mail.
+
+If the program is interactive, make it output a short notice like this
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+
+    Gnomovision version 69, Copyright (C) year  name of author
+    Gnomovision comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
+    This is free software, and you are welcome to redistribute it
+    under certain conditions; type `show c' for details.
+
+The hypothetical commands `show w' and `show c' should show the appropriate
+parts of the General Public License.  Of course, the commands you use may
+be called something other than `show w' and `show c'; they could even be
+mouse-clicks or menu items--whatever suits your program.
+
+You should also get your employer (if you work as a programmer) or your
+school, if any, to sign a "copyright disclaimer" for the program, if
+necessary.  Here is a sample; alter the names:
+
+  Yoyodyne, Inc., hereby disclaims all copyright interest in the program
+  `Gnomovision' (which makes passes at compilers) written by James Hacker.
+
+  <signature of Ty Coon>, 1 April 1989
+  Ty Coon, President of Vice
+
+This General Public License does not permit incorporating your program into
+proprietary programs.  If your program is a subroutine library, you may
+consider it more useful to permit linking proprietary applications with the
+library.  If this is what you want to do, use the GNU Library General
+Public License instead of this License.

INSTALL

+How to install?
+---------------
+- You'll need a web server and an existing PHP and MySQL installation.
+  If you require help on installation of these packages please visit
+  <http://httpd.apache.org>, <http://php.net> and <http://mysql.com>.
+
+- Move all refbase-0.9.7 files to your web directory.
+
+- Open the file 'initialize/db.inc.php' in a text editor and edit the values
+  of the variables '$databaseName', '$username' and '$password' to fit your
+  needs.
+  (Note that you might be able to use the refbase package without modifying
+   these variables, but we highly recommend not to use the default values!)
+
+- Now, open a web browser and access the 'install.php' script by typing:
+
+    <http://SERVER_ADDRESS/PATH_ON_SERVER/install.php>
+
+  (where the string 'SERVER_ADDRESS' is replaced by your server name and
+   'PATH_ON_SERVER' is the actual path to your refbase-0.9.7 web directory)
+
+  This should bring up the install form. Edit the contents of all text entry
+  fields to match your server setup and supply the MySQL admin password, then
+  click the 'Install' button to complete the installation process.
+
+  WIN32: Be sure to set a password for the MySQL root user. The path to MySQL
+         is probably '/Program Files/MySQL/bin/mysql.exe' or
+         '/wamp/mysql/bin/mysql.exe', or wherever you've installed MySQL.
+
+- Please delete 'install.php' and 'update.php' from your webserver.
+
+Solutions for known problems and general troubleshooting tips are given at:
+  <http://troubleshooting.refbase.net>
+
+See also:
+  <http://requirements.refbase.net>
+  <http://install.refbase.net>
+
+
+
+How to setup your own admin user?
+---------------------------------
+- After you've successfully installed the database (see above), open the main
+  page ('index.php') and login with:
+
+    Email     =  user@refbase.net
+    Password  =  start
+
+  You should now see a welcome message at the top right corner of the page
+  confirming your successful login.
+
+- Click on 'Add User' which should bring up an empty form. At a minimum, you
+  have to specify the admin's first name & last name, his institutional
+  abbreviation as well as his email address and password. Then click the 'Add
+  User' button. You will be shown a receipt page with the account details you
+  just entered.
+
+- Now open the file 'initialize/ini.inc.php' in a text editor and change the
+  value of the '$adminLoginEmail' variable to the email address you've
+  specified for your new admin user.
+
+- Log out from the database, then login again using the email address and
+  password of your newly created admin account.
+
+- You can now delete the initial user by choosing 'Manage Users' and clicking
+  the appropriate trash icon. (However, we recommend to keep this user until
+  you've explored the example records that come with the database)
+
+See also:
+  <http://adduser.refbase.net>
+
+
+
+How to configure the database?
+------------------------------
+In order to properly configure your database you'll need to edit the global
+configuration file:
+
+- Open the file 'initialize/ini.inc.php' & edit all values of the contained
+  variables to fit your needs. Please see the comments within the file for
+  further guidance.
+
+  Especially note that if you've chosen 'utf8' (Unicode) as default character
+  set on installation, you must re-save the file 'ini.inc.php' with Unicode
+  encoding (UTF-8, no BOM) and set variable '$contentTypeCharset' to 'UTF-8'.
+
+See also:
+  <http://configure.refbase.net>
+
+
+
+Import Options
+--------------
+refbase offers batch import of records via the web interface ('import.php') or
+the command line ('contrib/command_line/refbase_import'). These scripts allow
+to import records from various common bibliographic formats (BibTeX, Copac,
+Endnote (tagged text & XML), MODS XML, RefWorks, RIS or SciFinder) as well as
+from online databases (CSA Illumina, ISI Web of Science or PubMed (MEDLINE & XML)).
+
+If you're coming from Endnote you may want to try out the Endnote style file
+and PHP script that's included with refbase. This style file and PHP script
+allows Endnote users to transfer data into refbase at the command line (see
+the README file in the 'contrib/endnote' directory for further information).
+
+In addition, refbase allows PHP developers to write their own import parsers
+and use the provided templates to import their records into the refbase
+database (see the 'contrib/import_templates' directory for available
+templates).
+
+If you can't use any of the above mentioned import options, you might be able
+to convert your data into a tab-delimited text format that can be imported
+directly into the MySQL database. Here are some notes how to prepare
+tab-delimited data for direct upload into your newly created MySQL tables:
+
+- Fields are separated by tabs, records are separated by returns
+  (if not specified otherwise within the LOAD DATA statement).
+
+- The order of fields must resemble the field order specified in the MySQL
+  table 'refs'. Field information for table 'refs' is given at:
+    <http://wiki.refbase.net/index.php/Table_refs>
+
+- DATE format must be YYYY-MM-DD and TIME format must be HH:MM:SS.
+
+- Carriage returns *within* fields must be represented by a newline character
+  ('\n', ASCII character 10).
+
+- Empty fields must be indicated by \N.
+
+- Character encoding: if you've chose 'latin1' as default character set upon
+  installation, higher ASCII chars must be encoded as ISO-8859-1 aka 'Western
+  (ISO Latin 1)', otherwise data should be encoded as Unicode (UTF-8, no BOM).
+
+- File encoding must be UNIX.
+
+- Assuming your data file is named 'refs.txt', you should be able to upload
+  your data via use of the 'mysql' command line interpreter:
+
+    LOAD DATA LOCAL INFILE "/PATH/TO/FILE/refs.txt" INTO TABLE refs;
+
+  or, alternatively, use something like the following from your shell:
+
+    mysqlimport --local -u root -p YOUR_DB_NAME "/PATH/TO/FILE/refs.txt"
+
+  Note that if you're going to use the mysqlimport data import program the
+  data file *must* be named 'refs.txt'.
+
+See also:
+  <http://import.refbase.net>
+
+
+
+Skins
+-----
+refbase ships with alternative skins to change the appearance of the program.
+These are in the 'contrib/skins' directory. You can replace your
+'includes/header.inc.php', 'includes/footer.inc.php' with these. You may also
+need to copy files to the 'css' directory.
+
+Please contribute other skins to <info@refbase.net>.
+
+
+
+Extensions for other software
+-----------------------------
+In 'contribs/mediawiki', there is an extension for MediaWiki to more easily
+include reference information from refbase in a wiki page. This will also
+allow you to use Wikipedia's citation templates, which may have an appearance
+that you like or might be easier for you (and the other users of your wiki) to
+customize.
+

README

+refbase 0.9.7 README
+====================
+
+About refbase
+-------------
+  refbase is a web-based solution for managing scientific literature,
+  references and citations.
+  
+  Currently, the following features have been implemented for:
+  EVERYONE
+    - search the database using different search forms
+    - search within results
+    - browse found records and sort results by any database field
+    - view results in different views (list view, citations, details,
+      print view)
+    - display results in different citation styles & output formats
+    - export selected records to XML (Atom, MODS, OAI_DC, ODF) and (via
+      the GPLed Bibutils programs) to ADS, BibTeX, EndNote, ISI, RIS and
+      Word XML
+    - display rich text (i.e., italics, super/sub-script, greek letters)
+    - extract citations from a text & build an appropriate reference list
+    - track additions via RSS and generate custom RSS feeds from searches
+    - web services (SRU & OpenSearch) that allow clients to access a
+      refbase database using a standard query syntax and retrieve results
+      in structured XML format
+    - dissemination of bibliographic data via standard methods (COinS &
+      unAPI) allowing clients to automatically discover and extract data
+      from refbase
+    - search a refbase online database from the command line and retrieve
+      results in various export & citation formats
+  LOGGED IN USERS
+    - user-specific fields which are stored individually for each user
+    - import of records from common bibliographic formats and online
+      databases via the web interface or the command line
+    - automatic email announcements for newly added records
+    - save and recall search queries
+    - adding records to user-specific groups
+    - add/edit/delete records as well as file upload & download links
+  ADMINISTRATOR
+    - user management interface provided to the database admin
+    - set access permissions on a per-user basis
+
+  More information is given at:
+    <http://features.refbase.net>
+
+Credits
+-------
+  See AUTHORS
+
+Requirements
+------------
+  refbase requires:
+  - a web server (like the Apache HTTP Server <http://httpd.apache.org/>)
+  - PHP <http://www.php.net/> (version 5.2.0 or greater) with enabled
+    session support & installed PHP MySQL module
+  - MySQL <http://www.mysql.com/> (version 4.1.x or greater required for
+    Unicode support)
+  
+  - for import and export of various formats (e.g., Endnote & BibTeX):
+    Bibutils <http://www.refbase.net/index.php/Bibutils>
+    (version 3.21 or greater)
+
+  More detailed information is available at:
+    <http://requirements.refbase.net>
+
+Installation & Import
+---------------------
+  See INSTALL
+
+Update
+------
+  See UPDATE
+
+New Features
+------------
+  See NEWS
+
+Changelog
+---------
+  See ChangeLog
+
+Known issues
+------------
+  See BUGS
+
+What is missing?
+----------------
+  See TODO
+
+License
+-------
+  See COPYING
+
+Further information
+-------------------
+  For more information about the refbase project and pointers to working
+  examples of refbase please visit:
+    <http://www.refbase.net/>  or  <http://refbase.sourceforge.net/>

TODO

+Suggestions for improving refbase:
+
+- Open up the refbase group (aka tagging) mechanism so that groups can be made
+  public, group-specific or private.
+
+- Improved search capabilities which, e.g., allow for 'OR' searches and/or a
+  Google-like search syntax. One possible solution might be to offer support for
+  the Contextual Query Language (CQL) across the entire interface. More flexible
+  handling of accented characters and umlauts would be also desirable.
+
+- Offer means to auto-detect duplicates on import, link duplicate entries with
+  their original ones and allow users to migrate their user-specific data from a
+  duplicate record to the original. It would be also nice if duplicate records
+  could be hidden from the interface.
+
+- Improve the installation process so that the web-based installer works with
+  more server setups (including installation on shared hosts), and allows
+  setting important config options via the web interface.
+
+- More user-specific and record-specific rights management.
+
+- Provide additional citation styles, preferably via the use of a plugin
+  mechanism which would make it easy to add or edit citation styles. Support for
+  the Citation Style Language (CSL) would be desirable.
+
+- Increase number of supported resource types and allow users to add their own
+  types. A hierarchical system with basic fallback types would be desirable.
+
+- Provide a machine-readable interface (API) that not only allows clients to
+  query a refbase database and retrieve results in a structured format, but that
+  also allows modification of any database information.
+
+- Provide better integration with desktop reference managers so that users could
+  search an online refbase database from within their desktop application, or
+  upload (and eventually synch) records to a refbase server directly from within
+  their desktop application.
+
+- Upon add/edit, offer to auto-fill empty fields based on information available
+  in other fields/records/tables or via web services. Eventually, such a system
+  could also be used to validate data that were entered/imported by the user.
+
+- Simplify manual data input by providing record type specific forms. These
+  forms could guide a user by only showing (or at least indicating) those fields
+  that are required for a particular record type (like journal articles, book
+  chapters or whole books).
+
+- Allow users to upload multiple files per record.
+
+- Allow users to specify multiple URLs for the same record, and eventually
+  provide a customizable system for auto-generation of links (based on the
+  record's metadata).
+
+- Store record identifiers from foreign repositories (e.g. arXiv.org or
+  PubMed.gov) in some dedicated field(s), which would allow to easily
+  auto-generate links back to these repositories.
+
+- Implement the OAI Protocol for Metadata Harvesting which would provide (yet
+  another) standard way for software to retrieve information from refbase.
+
+- More localizations, i.e. translations of the refbase interface into other
+  languages.
+
+- Cross-site searches (both through other copies of refbase and through other
+  bibliographic databases).
+
+- Refactor for more code reuse (share more between cite/list/details views,
+  etc.), and eventually modularize the code to allow for other RDBMS, custom
+  database schemes and/or a plugin mechanism.
+
+- Provide better interface customization via a templating/skin mechanism and/or
+  improved CSS styling.
+
+- Allow the admin to add any custom fields and/or alter the layout of available
+  fields.
+
+- More embedding of citation metadata in HTML pages in a machine-readable form
+  (such as embedded RDF or microformats) which may be processed by clients.
+
+- Improved export through both revisions to the current MODS XML/bibutils system
+  and through adding more native export options which wouldn't require bibutils.
+
+- User customization: provide a user-specific preferences page where one could
+  specify the default view and the default columns that are visible in query
+  results or the default fields that are visible in particular search forms.
+
+- Easier import of bibliographic data from web sources via bookmarklets and/or
+  scrapers.
+
+- Offer a notes/comment system where multiple notes (of unlimited length) would
+  be allowed for a particular record and where notes would be searchable, and
+  could be made public, group-specific or private.
+
+- Enable remembering of marked records across different requests.
+
+- Provide an administrative interface to deleted records.
+
+A more detailed list of planned feature additions is given at:
+  <http://additions.refbase.net>

UPDATE

+Please follow the steps below to update an existing refbase installation to
+refbase-0.9.7. The update script should also be able to update any refbase
+version that was installed from SVN prior to the release of refbase-0.9.7. To
+update versions of refbase prior to refbase-0.8.0, please update to
+refbase-0.8.0 first.
+
+- First of all, please make sure that you have a recent backup of your refbase
+  MySQL database! This can be accomplished by issuing the following command
+  from your shell:
+
+    mysqldump DATABASE_NAME -uADMINUSER -p --complete-insert --opt > refbase.sql
+
+  In the above line, replace DATABASE_NAME with the database name that you've
+  specified for the variable '$databaseName' (in file
+  'initialize/db.inc.php'). Similarly, replace ADMINUSER with the name of the
+  administrative user that has full access to the refbase MySQL database. As
+  an example, if the variable '$databaseName' is set to "literature" and your
+  administrative user is "root", the above line would read:
+
+    mysqldump literature -uroot -p --complete-insert --opt > refbase.sql
+
+  WARNING: If using MySQL 4.1.x, mysqldump's charset conversion may damage
+           data. If necessary, use the '--default-character-set=latin1' option
+           to avoid the conversion. More info is available at
+           <http://backup.refbase.net>.
+
+- Backup your original configuration files 'initialize/db.inc.php' and
+  'initialize/ini.inc.php'. Optionally, you may want to backup all of your
+  existing refbase scripts.
+
+- Move all refbase-0.9.7 files to your server's web directory.
+
+- Open the file 'initialize/db.inc.php' in a text editor and re-enter the
+  values from your old 'db.inc.php' file for the variables '$databaseName',
+  '$username' and '$password'. Similarly, migrate all custom values that
+  you've entered within the old 'ini.inc.php' file to the new one.
+
+- Now, open a web browser and access the 'update.php' script by typing:
+
+    <http://SERVER_ADDRESS/PATH_ON_SERVER/update.php>
+
+   (where the string 'SERVER_ADDRESS' is replaced by your server name and
+    'PATH_ON_SERVER' is the actual path to your refbase-0.9.5 web directory)
+
+  This should bring up the update form. Edit the contents of all text entry
+  fields to match your server setup and supply the MySQL admin password, then
+  click the 'Update' button to update the database.
+
+  WIN32: Be sure to set a password for the MySQL root user.
+
+  This will add the MySQL tables that were added in 0.9.x and alter existing
+  tables to match the table design used by refbase-0.9.x. A detailed log is
+  generated for all performed update actions. Your data should remain
+  untouched by this operation.
+
+- After you've successfully performed the update, please remove the files
+  'update.php' & 'update.sql' (as well as 'install.php' & 'install.sql') from
+  your web directory.
+
+- Note: The update process modifies some existing formats in table 'formats'
+  and adds additional ones. Please login as admin and make sure that suitable
+  import, export and citation formats are enabled for all of your users within
+  the "Display Options" section of the admin interface.
+
+See also:
+  <http://update.refbase.net>

cite/formats/cite_ascii.php

+<?php
+	// Project:    Web Reference Database (refbase) <http://www.refbase.net>
+	// Copyright:  Matthias Steffens <mailto:refbase@extracts.de> and the file's
+	//             original author(s).
+	//
+	//             This code is distributed in the hope that it will be useful,
+	//             but WITHOUT ANY WARRANTY. Please see the GNU General Public
+	//             License for more details.
+	//
+	// File:       ./cite/formats/cite_ascii.php
+	// Repository: $HeadURL: https://svn.code.sf.net/p/refbase/code/branches/bleeding-edge/cite/formats/cite_ascii.php $
+	// Author(s):  Matthias Steffens <mailto:refbase@extracts.de>
+	//
+	// Created:    10-Jun-06, 02:54
+	// Modified:   $Date: 2012-02-27 21:25:30 +0100 (Mon, 27 Feb 2012) $
+	//             $Author: msteffens $
+	//             $Revision: 1337 $
+
+	// This is a citation format file (which must reside within the 'cite/formats/' sub-directory of your refbase root directory). It contains a
+	// version of the 'citeRecords()' function that outputs a reference list from selected records in plain text format. Plain text output is
+	// mainly meant for command line interfaces such as the refbase command line client (<http://cli.refbase.net/>).
+
+	// --------------------------------------------------------------------
+
+	// --- BEGIN CITATION FORMAT ---
+
+	function citeRecords($result, $rowsFound, $query, $queryURL, $showQuery, $showLinks, $rowOffset, $showRows, $previousOffset, $nextOffset, $wrapResults, $citeStyle, $citeOrder, $citeType, $orderBy, $headerMsg, $userID, $viewType)
+	{
+		global $officialDatabaseName; // these variables are defined in 'ini.inc.php'
+		global $databaseBaseURL;
+		global $contentTypeCharset;
+
+		global $client;
+
+		// The array '$transtab_refbase_ascii' contains search & replace patterns for conversion from refbase markup to plain text
+		global $transtab_refbase_ascii; // defined in 'transtab_refbase_ascii.inc.php'
+
+		$plainTextData = ""; // make sure that our buffer variable is empty
+
+		// Header:
+		if (!empty($headerMsg))
+		{
+			// Decode any HTML entities:
+			// (these may occur in the header message e.g. if the user's preferred display language is not English but German or French, etc)
+			$headerMsg = decodeHTML($contentTypeCharset, $headerMsg); // function 'decodeHTML()' is defined in 'include.inc.php', and '$contentTypeCharset' is defined in 'ini.inc.php'
+
+			// Convert refbase markup in the header message into plain text:
+			$headerMsg = searchReplaceText($transtab_refbase_ascii, $headerMsg, true); // function 'searchReplaceText()' is defined in 'include.inc.php'
+
+			$plainTextData .= "$headerMsg\n\n"; // prefix any passed header message
+		}
+
+		// Initialize array variables:
+		$yearsArray = array();
+		$typeTitlesArray = array();
+
+		// Define inline text markup to be used by the 'citeRecord()' function:
+		$markupPatternsArray = array("bold-prefix"        => "", // for plain text output, we'll omit any font-shape markup
+		                             "bold-suffix"        => "",
+		                             "italic-prefix"      => "",
+		                             "italic-suffix"      => "",
+		                             "underline-prefix"   => "",
+		                             "underline-suffix"   => "",
+		                             "endash"             => "-",
+		                             "emdash"             => "-",
+		                             "ampersand"          => "&",
+		                             "double-quote"       => '"',
+		                             "double-quote-left"  => '"',
+		                             "double-quote-right" => '"',
+		                             "single-quote"       => "'",
+		                             "single-quote-left"  => "'",
+		                             "single-quote-right" => "'",
+		                             "less-than"          => "<",
+		                             "greater-than"       => ">",
+		                             "newline"            => "\n"
+		                            );
+
+		// Defines search & replace 'actions' that will be applied upon TEXT output to all those refbase fields that are listed
+		// in the corresponding 'fields' element:
+		$plainTextSearchReplaceActionsArray = array(
+		                                            array('fields'  => array("title", "publication", "abbrev_journal", "address", "keywords", "abstract", "orig_title", "series_title", "abbrev_series_title", "notes"),
+		                                                  'actions' => $transtab_refbase_ascii
+		                                                 )
+		                                           );
+
+		// For CLI queries, we'll allow paging thru the result set, i.e. we honour the values of the CLI options '-S|--start' ('$rowOffset')
+		// and '-R|--rows' ('$showRows') ('$rowOffset' and '$showRows' are re-assigned in function 'seekInMySQLResultsToOffset()' in 'include.inc.php')
+		if (preg_match("/^cli/i", $client)) // if the query originated from a command line client such as the "refbase" CLI client ("cli-refbase-1.0")
+			$showMaxRows = $showRows; // show only rows up to the value given in '$showRows'
+		else
+			$showMaxRows = $rowsFound; // otherwise show all rows
+
+
+		// LOOP OVER EACH RECORD:
+		// Fetch one page of results (or less if on the last page)
+		// (i.e., upto the limit specified in $showMaxRows) fetch a row into the $row array and ...
+		for ($rowCounter=0; (($rowCounter < $showMaxRows) && ($row = @ mysql_fetch_array($result))); $rowCounter++)
+		{
+			foreach ($row as $rowFieldName => $rowFieldValue)
+				// Apply search & replace 'actions' to all fields that are listed in the 'fields' element of the arrays contained in '$plainTextSearchReplaceActionsArray':
+				foreach ($plainTextSearchReplaceActionsArray as $fieldActionsArray)
+					if (in_array($rowFieldName, $fieldActionsArray['fields']))
+						$row[$rowFieldName] = searchReplaceText($fieldActionsArray['actions'], $row[$rowFieldName], true); // function 'searchReplaceText()' is defined in 'include.inc.php'
+
+
+			// Order attributes according to the chosen output style & record type:
+			$record = citeRecord($row, $citeStyle, $citeType, $markupPatternsArray, false); // function 'citeRecord()' is defined in the citation style file given in '$citeStyleFile' (which, in turn, must reside in the 'cite' directory of the refbase root directory), see function 'generateCitations()'
+
+
+			// Print out the current record:
+			if (!empty($record)) // unless the record buffer is empty...
+			{
+				// Print any section heading(s):
+				if (preg_match("/year|type/i", $citeOrder))
+				{
+					list($yearsArray, $typeTitlesArray, $sectionHeading) = generateSectionHeading($yearsArray, $typeTitlesArray, $row, $citeOrder, "", "", "", "\n\n", "", "\n\n"); // function 'generateSectionHeading()' is defined in 'cite.inc.php'
+
+					$plainTextData .= $sectionHeading;
+				}
+
+				// Write plain TEXT paragraph:
+				if (preg_match("/^cli/i", $client)) // when outputting results to a command line client, we'll prefix the record with it's serial number (and it's user-specific cite key, if available)
+				{
+					// This is a stupid hack that maps the names of the '$row' array keys to those used
+					// by the '$formVars' array (which is required by function 'generateCiteKey()')
+					// (eventually, the '$formVars' array should use the MySQL field names as names for its array keys)
+					$formVars = buildFormVarsArray($row); // function 'buildFormVarsArray()' is defined in 'include.inc.php'
+
+					// Generate or extract the cite key for this record:
+					// NOTE: currently, the following placeholders are not available for citation output:
+					//       <:keywords:>, <:issn:>, <:area:>, <:notes:>, <:userKeys:>
+					//       if the cite key specification uses one of these placeholders, it will get ignored
+					$citeKey = generateCiteKey($formVars); // function 'generateCiteKey()' is defined in 'include.inc.php'
+
+					$plainTextData .= "[" . $row['serial'] . "] ";
+
+					if (!empty($citeKey))
+						// Use the custom cite key that's been build according to the user's individual export options:
+						$plainTextData .= "{" . $citeKey . "} ";
+				}
+
+				$plainTextData .= $record . "\n\n"; // create paragraph with encoded record text
+			}
+		}
+
+		if (preg_match("/^cli/i", $client)) // when outputting results to a command line client, we'll append some info about the number of rows displayed/found, the database name/URL and optionally display the SQL query
+		{
+			// Calculate the maximum result number on each page:
+			if (($rowOffset + $showRows) < $rowsFound)
+				$showMaxRow = ($rowOffset + $showRows); // maximum result number on each page
+			else
+				$showMaxRow = $rowsFound; // for the last results page, correct the maximum result number if necessary
+
+			if ($rowsFound == 1)
+				$footerInfoPart = " record found";
+			else
+				$footerInfoPart = " records found";
+
+			$rowsFoundInfo = ($rowOffset + 1) . "-" . $showMaxRow . " of " . $rowsFound . $footerInfoPart; // prints e.g. "1-5 of 23 records found"
+
+			$rowsFoundDelimiter = preg_replace("/./i", "-", $rowsFoundInfo); // generate a line of hyphens which has the same length as the string in '$rowsFoundInfo' (e.g. "-----------------------")
+
+			$plainTextData .= $rowsFoundDelimiter . "\n" . $rowsFoundInfo . "\n\n"; // append info about rows displayed/found
+
+			$plainTextData .= $officialDatabaseName . "\n" . $databaseBaseURL . "\n\n"; // append database name and URL (comment this line if you don't like that)
+
+			if ($showQuery == "1") // display SQL query:
+				$plainTextData .= "Query: " . $query . "\n\n";
+		}
+
+
+		return $plainTextData;
+	}
+
+	// --- END CITATION FORMAT ---
+?>

cite/formats/cite_latex.php

+<?php
+	// Project:    Web Reference Database (refbase) <http://www.refbase.net>
+	// Copyright:  Matthias Steffens <mailto:refbase@extracts.de> and the file's
+	//             original author(s).
+	//
+	//             This code is distributed in the hope that it will be useful,
+	//             but WITHOUT ANY WARRANTY. Please see the GNU General Public
+	//             License for more details.
+	//
+	// File:       ./cite/formats/cite_latex.php
+	// Repository: $HeadURL: https://svn.code.sf.net/p/refbase/code/branches/bleeding-edge/cite/formats/cite_latex.php $
+	// Author(s):  Matthias Steffens <mailto:refbase@extracts.de>
+	//
+	// Created:    10-Jun-06, 02:32
+	// Modified:   $Date: 2012-02-27 21:25:30 +0100 (Mon, 27 Feb 2012) $
+	//             $Author: msteffens $
+	//             $Revision: 1337 $
+
+	// This is a citation format file (which must reside within the 'cite/formats/' sub-directory of your refbase root directory). It contains a
+	// version of the 'citeRecords()' function that outputs a reference list from selected records in LaTeX format.
+	// 
+
+	// --------------------------------------------------------------------
+
+	// --- BEGIN CITATION FORMAT ---
+
+	function citeRecords($result, $rowsFound, $query, $queryURL, $showQuery, $showLinks, $rowOffset, $showRows, $previousOffset, $nextOffset, $wrapResults, $citeStyle, $citeOrder, $citeType, $orderBy, $headerMsg, $userID, $viewType)
+	{
+		global $contentTypeCharset; // defined in 'ini.inc.php'
+
+		global $client;
+
+		// The array '$transtab_refbase_latex' contains search & replace patterns for conversion from refbase markup to LaTeX markup & entities.
+		// Converts refbase fontshape markup (italic, bold) into LaTeX commands of the 'textcomp' package, super- and subscript as well as greek
+		// symbols get converted into the respective commands in math mode. You may need to adopt the LaTeX markup to suit your individual needs.
+		global $transtab_refbase_latex; // defined in 'transtab_refbase_latex.inc.php'
+
+		// The arrays '$transtab_latin1_latex' and '$transtab_unicode_latex' provide translation tables for best-effort conversion of higher ASCII
+		// characters from ISO-8859-1 (or Unicode, respectively) to LaTeX entities.
+		global $transtab_latin1_latex; // defined in 'transtab_latin1_latex.inc.php'
+		global $transtab_unicode_latex; // defined in 'transtab_unicode_latex.inc.php'
+
+		// Initialize array variables:
+		$yearsArray = array();
+		$typeTitlesArray = array();
+
+		// Define inline text markup to be used by the 'citeRecord()' function:
+		$markupPatternsArray = array("bold-prefix"        => "\\textbf{",
+		                             "bold-suffix"        => "}",
+		                             "italic-prefix"      => "\\textit{",
+		                             "italic-suffix"      => "}",
+		                             "underline-prefix"   => "\\ul{", // the '\ul' command requires '\usepackage{soul}'
+		                             "underline-suffix"   => "}",
+		                             "endash"             => "--", // or use '{\\textendash}'
+		                             "emdash"             => "---", // or use '{\\textemdash}'
+		                             "ampersand"          => "&", // conversion of ampersands is done below, after the citation has been generated
+		                             "double-quote"       => '"',
+		                             "double-quote-left"  => "{\\textquotedblleft}",
+		                             "double-quote-right" => "{\\textquotedblright}",
+		                             "single-quote"       => "'", // same as for ampersands
+		                             "single-quote-left"  => "{\\textquoteleft}",
+		                             "single-quote-right" => "{\\textquoteright}",
+		                             "less-than"          => "<",
+		                             "greater-than"       => ">",
+		                             "newline"            => "\n\n"
+		                            );
+
+		// Defines search & replace 'actions' that will be applied upon LaTeX output to all those refbase fields that are listed
+		// in the corresponding 'fields' element:
+		$latexSearchReplaceActionsArray = array(
+		                                        array('fields'  => array("title", "publication", "abbrev_journal", "address", "keywords", "abstract", "orig_title", "series_title", "abbrev_series_title", "notes"),
+		                                              'actions' => $transtab_refbase_latex
+		                                             )
+		                                       );
+
+		// For CLI queries, we'll allow paging thru the result set, i.e. we honour the values of the CLI options '-S|--start' ('$rowOffset')
+		// and '-R|--rows' ('$showRows') ('$rowOffset' and '$showRows' are re-assigned in function 'seekInMySQLResultsToOffset()' in 'include.inc.php')
+		if (preg_match("/^cli/i", $client)) // if the query originated from a command line client such as the "refbase" CLI client ("cli-refbase-1.0")
+			$showMaxRows = $showRows; // show only rows up to the value given in '$showRows'
+		else
+			$showMaxRows = $rowsFound; // otherwise show all rows
+
+
+		// Setup the basic LaTeX document structure:
+		$latexData = "%&LaTeX\n"
+		           . "\\documentclass{article}\n\n";
+
+		// NOTE: the "Vancouver" & "Harvard 1" citation styles make use of the '\ul' command which requires '\usepackage{soul}'
+		// TODO: figure out a better logic when to include the '\usepackage{soul}' statement (or should we simply always include it?)
+		if (preg_match("/^(Vancouver|Harvard 1)$/i", $citeStyle))
+			$latexData .= "\\usepackage{soul}\n";
+
+		if ($contentTypeCharset == "UTF-8")
+			$latexData .= "\\usepackage[utf8]{inputenc}\n";
+		else
+			$latexData .= "\\usepackage[latin1]{inputenc}\n";
+
+		$latexData .= "\\usepackage[T1]{fontenc}\n"
+		            . "\\usepackage{textcomp}\n\n";
+
+		$latexData .= "\\begin{document}\n\n";
+
+		// Header:
+		if (!empty($headerMsg))
+		{
+			// Remove any colon (":") from end of header message:
+			$headerMsg = trimTextPattern($headerMsg, ":", false, true); // function 'trimTextPattern()' is defined in 'include.inc.php'
+
+			// Decode any HTML entities:
+			// (these may occur in the header message e.g. if the user's preferred display language is not English but German or French, etc)
+			$headerMsg = decodeHTML($contentTypeCharset, $headerMsg); // function 'decodeHTML()' is defined in 'include.inc.php', and '$contentTypeCharset' is defined in 'ini.inc.php'
+
+			// Convert refbase markup in the header message into appropriate LaTeX markup & entities:
+			$headerMsg = searchReplaceText($transtab_refbase_latex, $headerMsg, true); // function 'searchReplaceText()' is defined in 'include.inc.php'
+
+			// Attempt to convert higher ASCII chars (i.e., characters with an ASCII value of >= 128) in the header message to their corresponding LaTeX entities:
+			if ($contentTypeCharset == "UTF-8")
+				$headerMsg = searchReplaceText($transtab_unicode_latex, $headerMsg, false);
+			else
+				$headerMsg = searchReplaceText($transtab_latin1_latex, $headerMsg, false);
+
+			$latexData .= "\\title{" . $headerMsg . "}\n\n"
+			            . "\\maketitle\n\n";
+		}
+
+		if (!preg_match("/type|year/i", $citeOrder))
+			$latexData .= "\\begin{thebibliography}{" . $showMaxRows . "}\n\n";
+
+
+		// LOOP OVER EACH RECORD:
+		// Fetch one page of results (or less if on the last page)
+		// (i.e., upto the limit specified in $showMaxRows) fetch a row into the $row array and ...
+		for ($rowCounter=0; (($rowCounter < $showMaxRows) && ($row = @ mysql_fetch_array($result))); $rowCounter++)
+		{
+			foreach ($row as $rowFieldName => $rowFieldValue)
+				// Apply search & replace 'actions' to all fields that are listed in the 'fields' element of the arrays contained in '$latexSearchReplaceActionsArray':
+				foreach ($latexSearchReplaceActionsArray as $fieldActionsArray)
+					if (in_array($rowFieldName, $fieldActionsArray['fields']))
+						$row[$rowFieldName] = searchReplaceText($fieldActionsArray['actions'], $row[$rowFieldName], true); // function 'searchReplaceText()' is defined in 'include.inc.php'
+
+
+			// Order attributes according to the chosen output style & record type:
+			$record = citeRecord($row, $citeStyle, $citeType, $markupPatternsArray, false); // function 'citeRecord()' is defined in the citation style file given in '$citeStyleFile' (which, in turn, must reside in the 'cite' directory of the refbase root directory), see function 'generateCitations()'
+
+
+			// Print out the current record:
+			if (!empty($record)) // unless the record buffer is empty...
+			{
+				// Print any section heading(s):
+				if (preg_match("/year|type/i", $citeOrder))
+				{
+					list($yearsArray, $typeTitlesArray, $sectionHeading) = generateSectionHeading($yearsArray, $typeTitlesArray, $row, $citeOrder, "", "", "\\section*{", "}\n\n", "\\subsection*{", "}\n\n"); // function 'generateSectionHeading()' is defined in 'cite.inc.php'
+
+					$latexData .= $sectionHeading;
+				}
+
+				// Attempt to convert higher ASCII chars (i.e., characters with an ASCII value of >= 128) to their corresponding LaTeX entities:
+				if ($contentTypeCharset == "UTF-8")
+					$recordEncoded = searchReplaceText($transtab_unicode_latex, $record, false); // function 'searchReplaceText()' is defined in 'include.inc.php'
+				else
+					$recordEncoded = searchReplaceText($transtab_latin1_latex, $record, false);
+
+				// Write LaTeX paragraph:
+				if (!preg_match("/type|year/i", $citeOrder))
+				{
+					// This is a stupid hack that maps the names of the '$row' array keys to those used
+					// by the '$formVars' array (which is required by function 'generateCiteKey()')
+					// (eventually, the '$formVars' array should use the MySQL field names as names for its array keys)
+					$formVars = buildFormVarsArray($row); // function 'buildFormVarsArray()' is defined in 'include.inc.php'
+
+					// Generate or extract the cite key for this record:
+					// NOTE: currently, the following placeholders are not available for citation output:
+					//       <:keywords:>, <:issn:>, <:area:>, <:notes:>, <:userKeys:>
+					//       if the cite key specification uses one of these placeholders, it will get ignored
+					$citeKey = generateCiteKey($formVars); // function 'generateCiteKey()' is defined in 'include.inc.php'
+
+					if (!empty($citeKey))
+						// Use the custom cite key that's been build according to the user's individual export options:
+						$latexData .= "\\bibitem{" . $citeKey . "} ";
+					else
+						// The '\bibitem' command requires a cite key, which is why we'll include the record's serial number
+						// even when the user's export options specify 'export_cite_keys=no' or 'autogenerate_cite_keys=no':
+						$latexData .= "\\bibitem{" . $row['serial'] . "} ";
+				}
+
+				$latexData .= $recordEncoded . "\n\n"; // create paragraph with encoded record text
+			}
+		}
+
+		if (!preg_match("/type|year/i", $citeOrder))
+			$latexData .= "\\end{thebibliography}\n\n";
+
+		$latexData .= "\\end{document}\n\n";
+
+		return $latexData;
+	}
+
+	// --- END CITATION FORMAT ---
+?>

cite/formats/cite_latex_bbl.php

+<?php
+	// Project:    Web Reference Database (refbase) <http://www.refbase.net>
+	// Copyright:  Matthias Steffens <mailto:refbase@extracts.de> and the file's
+	//             original author(s).
+	//
+	//             This code is distributed in the hope that it will be useful,
+	//             but WITHOUT ANY WARRANTY. Please see the GNU General Public
+	//             License for more details.
+	//
+	// File:       ./cite/formats/cite_latex_bbl.php
+	// Repository: $HeadURL$
+	// Author(s):  Matthias Steffens <mailto:refbase@extracts.de>
+	//
+	// Created:    20-Jul-07, 19:42
+	// Modified:   $Date: 2012-02-27 21:25:30 +0100 (Mon, 27 Feb 2012) $
+	//             $Author$
+	//             $Revision: 1337 $
+
+	// This is a citation format file (which must reside within the 'cite/formats/' sub-directory of your refbase root directory). It contains a version of
+	// the 'citeRecords()' function that outputs a reference list from selected records in LateX .bbl format, to be used with LaTeX/BibTeX. The .bbl file
+	// generated by refbase can be used as a replacement of the BibTeX-generated .bbl file. Make sure to use "citeOrder=author" when generating the .bbl file.
+
+	// NOTE: In its current incarnation, this script outputs a .bbl variant that is intended to be used with the natbib package.
+	//       You may want to adopt the style-specific settings below if necessary. The natbib package is available at:
+	//       <http://www.ctan.org/tex-archive/macros/latex/contrib/natbib/>
+
+	// --------------------------------------------------------------------
+
+	// --- BEGIN CITATION FORMAT ---
+
+	function citeRecords($result, $rowsFound, $query, $queryURL, $showQuery, $showLinks, $rowOffset, $showRows, $previousOffset, $nextOffset, $wrapResults, $citeStyle, $citeOrder, $citeType, $orderBy, $headerMsg, $userID, $viewType)
+	{
+		global $contentTypeCharset; // defined in 'ini.inc.php'
+
+		global $client;
+
+		// The array '$transtab_refbase_latex' contains search & replace patterns for conversion from refbase markup to LaTeX markup & entities.
+		// Converts refbase fontshape markup (italic, bold) into LaTeX commands of the 'textcomp' package, super- and subscript as well as greek
+		// symbols get converted into the respective commands in math mode. You may need to adopt the LaTeX markup to suit your individual needs.
+		global $transtab_refbase_latex; // defined in 'transtab_refbase_latex.inc.php'
+
+		// The arrays '$transtab_latin1_latex' and '$transtab_unicode_latex' provide translation tables for best-effort conversion of higher ASCII
+		// characters from ISO-8859-1 (or Unicode, respectively) to LaTeX entities.
+		global $transtab_latin1_latex; // defined in 'transtab_latin1_latex.inc.php'
+		global $transtab_unicode_latex; // defined in 'transtab_unicode_latex.inc.php'
+
+
+		// --- Begin style-specific settings ----------------------------------
+
+		// NOTE: the given settings are meant to be used with the natbib package;
+		//       you'll have to adopt these settings if you'd like to generate a
+		//       .bbl file for another style/package
+
+		// 1) Define header with .bst style-specific declarations:
+		// NOTE: since this header is normally inserted by BibTeX from the used .bst style, I'm not sure if there's a variant of this header that's
+		//       universally accepted by natbib. So, if necessary adopt it to your needs.
+		// -- by default, we use this header (as inserted by a .bst style that was generated from 'merlin.mbs' via the docstrip utility):
+		$bblHeader = "\\providecommand{\\natexlab}[1]{#1}" . "\n"
+		           . "\\providecommand{\\url}[1]{\\texttt{#1}}" . "\n"
+		           . "\\providecommand{\\urlprefix}{URL }" . "\n"
+		           . "\\providecommand{\\eprint}[2][]{\\url{#2}}" . "\n\n";
+
+		// -- here's another header example (as inserted by 'elsart-harv.bst'):
+//		$bblHeader = "\\expandafter\\ifx\\csname natexlab\\endcsname\\relax\\def\\natexlab#1{#1}\\fi" . "\n"
+//		           . "\\expandafter\\ifx\\csname url\\endcsname\\relax" . "\n"
+//		           . "  \\def\\url#1{\\texttt{#1}}\\fi" . "\n"
+//		           . "\\expandafter\\ifx\\csname urlprefix\\endcsname\\relax\\def\\urlprefix{URL }\\fi" . "\n\n";
+
+		// 2) Define name of \bibitem command:
+		$bibItemCommand = "\\bibitem"; // use "\\harvarditem" for the Harvard family of styles
+
+		// 3) Define variables and placeholder strings which together will form the \bibitem option string:
+
+		// -- variables:
+		$betweenShortAuthorsDelim = " & "; // used to connect individual author names in the short author list
+		$betweenFullAuthorsDelim = ", "; // used to connect multiple authors in the full author list
+		$betweenLastAuthorsDelim = " & "; // used to connect the second-to-last author with the last author in the full author list
+		$etalIdentifierString = " et~al."; // appended to the first author's last name if the record's number of authors exceeds the number given in '$maxAuthorCountInShortAuthorList'
+		$maxAuthorCountInShortAuthorList = 2; // maximum number of authors to be used in the short author list
+
+		// -- placeholder strings:
+		// (please see the refbase online documentation for more info about placeholders and their syntax: <http://placeholders.refbase.net/>)
+		$year = "<:year[4]:>"; // year format, e.g. "1990"
+		$shortAuthorList = "<:authors[" . $maxAuthorCountInShortAuthorList . "|" . $betweenShortAuthorsDelim . "|" . $etalIdentifierString .  "]:>"; // format of the short author list which is used as text citation, e.g. "Jones", "Jones and Baker" or "Jones et al."
+		$fullAuthorList = "<:authors[0|_#_§_~_|]:>"; // format of the full author list, e.g. "Jones, Baker, and Williams"
+		// NOTE: in the above placeholder string, we use the string "_#_§_~_" as author delimiter which allows us to uniquely identify that delimiter again below, and replace it with the contents of either '$betweenFullAuthorsDelim' or '$betweenLastAuthorsDelim' (depending on its position)
+
+		// 4) Define \bibitem option format:
+
+		// -- extended natbib 5.3 style:
+		$bibItemOptionShort = "[{" . $shortAuthorList . "}(" . $year . ")" . "]"; // e.g.: \bibitem[{Jones et al.}(1990)]{key}...
+		$bibItemOptionFull = "[{" . $shortAuthorList . "}(" . $year . "){" . $fullAuthorList . "}]"; // e.g.: \bibitem[{Jones et al.}(1990){Jones, Baker, and Williams}]{key}...
+		// NOTE: since the author lists may contain parentheses, we need to enclose them in curly brackets to work around a natbib limitation
+
+		// -- native natbib style:
+//		$bibItemOptionShort = "[" . $shortAuthorList . "(" . $year . ")" . "]"; // e.g.: \bibitem[Jones et al.(1990)]{key}...
+//		$bibItemOptionFull = "";
+
+		// -- apalike style:
+//		$bibItemOptionShort = "[" . $shortAuthorList . ", " . $year . "]"; // e.g.: \bibitem[Jones et al., 1990]{key}...
+//		$bibItemOptionFull = "";
+
+		// -- newapa or chicago styles:
+//		$bibItemOptionShort = "[\\protect\\citeauthoryear{" . $fullAuthorList . "}{" . $shortAuthorList . "}{" . $year . "}" . "]"; // this assumes that it's not allowed to omit the full author list, though I dunno)
+//		$bibItemOptionFull = "[\\protect\\citeauthoryear{" . $fullAuthorList . "}{" . $shortAuthorList . "}{" . $year . "}" . "]"; // e.g.: \bibitem[\protect\citeauthoryear{Jones, Baker, and Williams}{Jones et al.}{1990}]{key}...
+
+		// -- named style:
+//		$bibItemOptionShort = "[\\protect\\citeauthoryear{" . $shortAuthorList . "}{" . $year . "}" . "]"; // e.g.: \bibitem[\protect\citeauthoryear{Jones et al.}{1990}]{key}...
+//		$bibItemOptionFull = "";
+
+		// -- astron style:
+//		$bibItemOptionShort = "[\\protect\\astroncite{" . $shortAuthorList . "}{" . $year . "}" . "]"; // e.g.: \bibitem[\protect\astroncite{Jones et al.}{1990}]{key}...
+//		$bibItemOptionFull = "";
+
+		// -- authordate style:
+//		$bibItemOptionShort = "[\\protect\\citename{" . $shortAuthorList . ", }" . $year . "]"; // e.g.: \bibitem[\protect\citename{Jones et al., }1990]{key}...
+//		$bibItemOptionFull = "";
+
+		// -- harvard style:
+//		$bibItemOptionShort = "[" . $shortAuthorList . "]{" . $fullAuthorList . "}{" . $year . "}"; // this assumes that it's not allowed to omit the full author list, though I dunno)
+//		$bibItemOptionFull = "[" . $shortAuthorList . "]{" . $fullAuthorList . "}{" . $year . "}"; // e.g.: \harvarditem[Jones et al.]{Jones, Baker, and Williams}{1990}{key}...
+
+		// 5) Define deduplication prefix and suffix strings:
+		//    Identical text citation strings get uniquified by appending letters to the year, e.g. duplicate occurrences
+		//    of "Jones et al. 1990" should become "Jones et al. 1990a" and "Jones et al. 1990b" in the final output.
+		//    These prefix/suffix strings will be inserted before/after the deduplication letter:
+		$dedupPrefix = "{\\natexlab{"; // these prefix/suffix strings are required by natbib; if any custom command (such as '\natexlab') is used, make sure that the command is also defined above in variable '$bblHeader'
+		$dedupSuffix = "}}";
+
+		// --- End style-specific settings ------------------------------------
+
+
+		// Initialize array variables:
+		$yearsArray = array();
+		$typeTitlesArray = array();
+		$bibItemsArray = array();
+
+		// Define inline text markup to be used by the 'citeRecord()' function:
+		$markupPatternsArray = array("bold-prefix"        => "\\textbf{",
+		                             "bold-suffix"        => "}",
+		                             "italic-prefix"      => "\\textit{",
+		                             "italic-suffix"      => "}",
+		                             "underline-prefix"   => "\\ul{", // the '\ul' command requires '\usepackage{soul}'
+		                             "underline-suffix"   => "}",
+		                             "endash"             => "--", // or use '{\\textendash}'
+		                             "emdash"             => "---", // or use '{\\textemdash}'
+		                             "ampersand"          => "&", // conversion of ampersands is done below, after the citation has been generated
+		                             "double-quote"       => '"',
+		                             "double-quote-left"  => "{\\textquotedblleft}",
+		                             "double-quote-right" => "{\\textquotedblright}",
+		                             "single-quote"       => "'", // same as for ampersands
+		                             "single-quote-left"  => "{\\textquoteleft}",
+		                             "single-quote-right" => "{\\textquoteright}",
+		                             "less-than"          => "<",
+		                             "greater-than"       => ">",
+		                             "newline"            => "\n\n"
+		                            );
+
+		// Defines search & replace 'actions' that will be applied upon LaTeX output to all those refbase fields that are listed
+		// in the corresponding 'fields' element:
+		$latexSearchReplaceActionsArray = array(
+		                                        array('fields'  => array("title", "publication", "abbrev_journal", "address", "keywords", "abstract", "orig_title", "series_title", "abbrev_series_title", "notes"),
+		                                              'actions' => $transtab_refbase_latex
+		                                             )
+		                                       );
+
+		// For CLI queries, we'll allow paging thru the result set, i.e. we honour the values of the CLI options '-S|--start' ('$rowOffset')
+		// and '-R|--rows' ('$showRows') ('$rowOffset' and '$showRows' are re-assigned in function 'seekInMySQLResultsToOffset()' in 'include.inc.php')
+		if (preg_match("/^cli/i", $client)) // if the query originated from a command line client such as the "refbase" CLI client ("cli-refbase-1.0")
+			$showMaxRows = $showRows; // show only rows up to the value given in '$showRows'
+		else
+			$showMaxRows = $rowsFound; // otherwise show all rows
+
+
+		// Setup the basic .bbl document structure:
+		$latexData = "\\begin{thebibliography}{" . $showMaxRows . "}\n\n";
+
+		// Add header with .bst style-specific declarations:
+		$latexData .= $bblHeader;
+
+
+		// LOOP OVER EACH RECORD:
+		// Fetch one page of results (or less if on the last page)
+		// (i.e., upto the limit specified in $showMaxRows) fetch a row into the $row array and ...
+		for ($rowCounter=0; (($rowCounter < $showMaxRows) && ($row = @ mysql_fetch_array($result))); $rowCounter++)
+		{
+			foreach ($row as $rowFieldName => $rowFieldValue)
+				// Apply search & replace 'actions' to all fields that are listed in the 'fields' element of the arrays contained in '$latexSearchReplaceActionsArray':
+				foreach ($latexSearchReplaceActionsArray as $fieldActionsArray)
+					if (in_array($rowFieldName, $fieldActionsArray['fields']))
+						$row[$rowFieldName] = searchReplaceText($fieldActionsArray['actions'], $row[$rowFieldName], true); // function 'searchReplaceText()' is defined in 'include.inc.php'
+
+
+			// Order attributes according to the chosen output style & record type:
+			$record = citeRecord($row, $citeStyle, $citeType, $markupPatternsArray, false); // function 'citeRecord()' is defined in the citation style file given in '$citeStyleFile' (which, in turn, must reside in the 'cite' directory of the refbase root directory), see function 'generateCitations()'
+
+
+			// Print out the current record:
+			if (!empty($record)) // unless the record buffer is empty...
+			{
+				// This is a stupid hack that maps the names of the '$row' array keys to those used
+				// by the '$formVars' array (which is required by function 'generateCiteKey()')
+				// (eventually, the '$formVars' array should use the MySQL field names as names for its array keys)
+				$formVars = buildFormVarsArray($row); // function 'buildFormVarsArray()' is defined in 'include.inc.php'
+
+				// Generate or extract the cite key for this record:
+				// NOTE: currently, the following placeholders are not available for citation output:
+				//       <:keywords:>, <:issn:>, <:area:>, <:notes:>, <:userKeys:>
+				//       if the cite key specification uses one of these placeholders, it will get ignored
+				$citeKey = generateCiteKey($formVars); // function 'generateCiteKey()' is defined in 'include.inc.php'
+
+				// The '\bibitem' command requires a cite key, which is why we'll include the record's serial number
+				// even when the user's export options specify 'export_cite_keys=no' or 'autogenerate_cite_keys=no':
+				// NOTE: maybe we should always generate a cite key here, even if 'export_cite_keys=no' or 'autogenerate_cite_keys=no'??
+				if (empty($citeKey))
+					$citeKey = $row['serial'];
+
+				// Generate the \bibitem option string that's used to build the proper text citation:
+				$bibItemOptionShortString = parsePlaceholderString($formVars, $bibItemOptionShort, "<:authors[2| and | et~al.]:><(:year:)>"); // function 'parsePlaceholderString()' is defined in 'include.inc.php'
+
+				if (!empty($bibItemOptionFull) AND preg_match("/^[^;]+(;[^;]+){" . $maxAuthorCountInShortAuthorList . "}/", $row['author'])) // if the 'author' field does contain more authors as specified in '$maxAuthorCountInShortAuthorList'
+				{
+					// include full author list:
+					$bibItemOptionString = parsePlaceholderString($formVars, $bibItemOptionFull, "<:authors[2| and | et~al.]:><(:year:)><:authors[0|, |]:>");
+					$bibItemOptionString = preg_replace("/_#_§_~_(?!.*?_#_§_~_)/", $betweenLastAuthorsDelim, $bibItemOptionString); // replace last occurrence of "_#_§_~_"
+					$bibItemOptionString = preg_replace("/_#_§_~_/", $betweenFullAuthorsDelim, $bibItemOptionString); // replace all other occurrences of "_#_§_~_"
+				}
+				else // only include short author list:
+					$bibItemOptionString = $bibItemOptionShortString;
+
+				// In case of duplicate text citation strings, append a letter to the year in the \bibitem option string as well as in the formatted reference:
+				// NOTE: - this is not fool proof and currently only works if there are no more than 26 duplicate text citations (letters a-z)
+				//       - the below replace actions get triggered on the first four-digit number that happens to be identical to the record's year, but depending on the reference format, this may not be the actual year of the reference but some other number!
+				for ($i=0; isset($bibItemsArray[$bibItemOptionShortString]); $i++)
+				{
+					// Update the existing \bibitem entry (that has an identical text citation string) and append an "a" to it's year items:
+					if ($i == 0)
+					{
+						$dedupPrefixQuoted = preg_quote($dedupPrefix, "/"); // escape meta characters (including '/' that is used as delimiter for the PCRE replace functions below and which gets passed as second argument)
+						$dedupSuffixQuoted = preg_quote($dedupSuffix, "/");
+
+						$oldBibItemOptionShortString = preg_replace("/^\[(.+)\]$/", "\\1", $bibItemOptionShortString); // remove square brackets from short \bibitem option string (which is required for the subsequent 'str_replace()' action to work with short and full option strings)
+						$newBibItemOptionShortString = preg_replace("/(" . $row['year'] . ")(" . $dedupPrefixQuoted . "[a-z]*" . $dedupSuffixQuoted . ")*/", "\\1" . $dedupPrefix . "a" . $dedupSuffix, $oldBibItemOptionShortString, 1);
+						$bibItemsArray[$bibItemOptionShortString] = str_replace($oldBibItemOptionShortString, $newBibItemOptionShortString, $bibItemsArray[$bibItemOptionShortString]);
+						$bibItemsArray[$bibItemOptionShortString] = preg_replace("/(" . $row['year'] . ")(" . $dedupPrefixQuoted . "[a-z]*" . $dedupSuffixQuoted . ")*(?!.*?" . $row['year'] . ")/", "\\1" . $dedupPrefix . "a" . $dedupSuffix, $bibItemsArray[$bibItemOptionShortString], 1); // note that this will fail if the formatted reference contains a number after the year that is identical to the year!
+					}
+
+					// Append a letter to the year items of the current \bibitem entry:
+					$bibItemOptionShortString = preg_replace("/(" . $row['year'] . ")(" . $dedupPrefixQuoted . "[a-z]*" . $dedupSuffixQuoted . ")*/e", "'\\1$dedupPrefix'.chr(98 + $i).'$dedupSuffix'", $bibItemOptionShortString, 1); // the 'e' modifier allows to execute PHP code within the replacement pattern
+					$bibItemOptionString = preg_replace("/(" . $row['year'] . ")(" . $dedupPrefixQuoted . "[a-z]*" . $dedupSuffixQuoted . ")*/e", "'\\1$dedupPrefix'.chr(98 + $i).'$dedupSuffix'", $bibItemOptionString, 1);
+					$record = preg_replace("/(" . $row['year'] . ")(" . $dedupPrefixQuoted . "[a-z]*" . $dedupSuffixQuoted . ")*/e", "'\\1$dedupPrefix'.chr(98 + $i).'$dedupSuffix'", $record, 1);
+				}
+
+
+				// Attempt to convert higher ASCII chars (i.e., characters with an ASCII value of >= 128) to their corresponding LaTeX entities:
+				if ($contentTypeCharset == "UTF-8")
+					$recordEncoded = searchReplaceText($transtab_unicode_latex, $record, false); // function 'searchReplaceText()' is defined in 'include.inc.php'
+				else
+					$recordEncoded = searchReplaceText($transtab_latin1_latex, $record, false);
+
+				// We have to make sure that the \bibitem option string also contains proper LaTeX entities:
+				if ($contentTypeCharset == "UTF-8")
+					$bibItemOptionStringEncoded = searchReplaceText($transtab_unicode_latex, $bibItemOptionString, false);
+				else
+					$bibItemOptionStringEncoded = searchReplaceText($transtab_latin1_latex, $bibItemOptionString, false);
+
+
+				// Copy the current \bibitem entry to the array of generated \bibitem entries:
+				$bibItemsArray[$bibItemOptionShortString] = $bibItemCommand . $bibItemOptionStringEncoded . "{" . $citeKey . "} " . $recordEncoded;
+			}
+		}
+
+		$latexData .= implode("\n\n", $bibItemsArray) . "\n\n";
+
+		$latexData .= "\\end{thebibliography}\n\n";
+
+		return $latexData;
+	}
+
+	// --- END CITATION FORMAT ---
+?>

cite/formats/cite_markdown.php

+<?php
+	// Project:    Web Reference Database (refbase) <http://www.refbase.net>
+	// Copyright:  Matthias Steffens <mailto:refbase@extracts.de> and the file's
+	//             original author(s).
+	//
+	//             This code is distributed in the hope that it will be useful,
+	//             but WITHOUT ANY WARRANTY. Please see the GNU General Public
+	//             License for more details.
+	//
+	// File:       ./cite/formats/cite_markdown.php
+	// Repository: $HeadURL: https://svn.code.sf.net/p/refbase/code/branches/bleeding-edge/cite/formats/cite_markdown.php $
+	// Author(s):  Matthias Steffens <mailto:refbase@extracts.de>
+	//
+	// Created:    10-Jun-06, 02:58
+	// Modified:   $Date: 2012-02-27 21:25:30 +0100 (Mon, 27 Feb 2012) $
+	//             $Author: msteffens $
+	//             $Revision: 1337 $
+
+	// This is a citation format file (which must reside within the 'cite/formats/' sub-directory of your refbase root directory). It contains a
+	// version of the 'citeRecords()' function that outputs a reference list from selected records in Markdown format. Markdown is a plain text
+	// formatting syntax as well as a software tool that converts the plain text formatting back to HTML (<http://daringfireball.net/projects/markdown/>)
+
+	// --------------------------------------------------------------------
+
+	// --- BEGIN CITATION FORMAT ---
+
+	function citeRecords($result, $rowsFound, $query, $queryURL, $showQuery, $showLinks, $rowOffset, $showRows, $previousOffset, $nextOffset, $wrapResults, $citeStyle, $citeOrder, $citeType, $orderBy, $headerMsg, $userID, $viewType)
+	{
+		global $contentTypeCharset; // defined in 'ini.inc.php'
+
+		global $client;
+
+		// The array '$transtab_refbase_markdown' contains search & replace patterns for conversion from refbase markup to Markdown markup & entities
+		global $transtab_refbase_markdown; // defined in 'transtab_refbase_markdown.inc.php'
+
+		$markdownData = ""; // make sure that our buffer variable is empty
+
+		// Header:
+		if (!empty($headerMsg))
+		{
+			// Decode any HTML entities:
+			// (these may occur in the header message e.g. if the user's preferred display language is not English but German or French, etc)
+			$headerMsg = decodeHTML($contentTypeCharset, $headerMsg); // function 'decodeHTML()' is defined in 'include.inc.php', and '$contentTypeCharset' is defined in 'ini.inc.php'
+
+			// Convert refbase markup in the header message into appropriate Markdown markup & entities:
+			$headerMsg = searchReplaceText($transtab_refbase_markdown, $headerMsg, true); // function 'searchReplaceText()' is defined in 'include.inc.php'
+
+			$markdownData .= "# $headerMsg #\n\n";
+		}
+
+		// Initialize array variables:
+		$yearsArray = array();
+		$typeTitlesArray = array();
+
+		// Define inline text markup to be used by the 'citeRecord()' function:
+		$markupPatternsArray = array("bold-prefix"        => "**",
+		                             "bold-suffix"        => "**",
+		                             "italic-prefix"      => "_",
+		                             "italic-suffix"      => "_",
+		                             "underline-prefix"   => "<u>",
+		                             "underline-suffix"   => "</u>",
+		                             "endash"             => "&ndash;",
+		                             "emdash"             => "&mdash;",
+		                             "ampersand"          => "&",
+		                             "double-quote"       => '"',
+		                             "double-quote-left"  => "&ldquo;",
+		                             "double-quote-right" => "&rdquo;",
+		                             "single-quote"       => "'",
+		                             "single-quote-left"  => "&lsquo;",
+		                             "single-quote-right" => "&rsquo;",
+		                             "less-than"          => "<",
+		                             "greater-than"       => ">",
+		                             "newline"            => "  \n"
+		                            );
+
+		// Defines search & replace 'actions' that will be applied upon Markdown output to all those refbase fields that are listed
+		// in the corresponding 'fields' element:
+		$markdownSearchReplaceActionsArray = array(
+		                                           array('fields'  => array("title", "publication", "abbrev_journal", "address", "keywords", "abstract", "orig_title", "series_title", "abbrev_series_title", "notes"),
+		                                                 'actions' => $transtab_refbase_markdown
+		                                                )
+		                                          );
+
+		// For CLI queries, we'll allow paging thru the result set, i.e. we honour the values of the CLI options '-S|--start' ('$rowOffset')
+		// and '-R|--rows' ('$showRows') ('$rowOffset' and '$showRows' are re-assigned in function 'seekInMySQLResultsToOffset()' in 'include.inc.php')
+		if (preg_match("/^cli/i", $client)) // if the query originated from a command line client such as the "refbase" CLI client ("cli-refbase-1.0")
+			$showMaxRows = $showRows; // show only rows up to the value given in '$showRows'
+		else
+			$showMaxRows = $rowsFound; // otherwise show all rows
+
+
+		// LOOP OVER EACH RECORD:
+		// Fetch one page of results (or less if on the last page)
+		// (i.e., upto the limit specified in $showMaxRows) fetch a row into the $row array and ...
+		for ($rowCounter=0; (($rowCounter < $showMaxRows) && ($row = @ mysql_fetch_array($result))); $rowCounter++)
+		{
+			foreach ($row as $rowFieldName => $rowFieldValue)
+				// Apply search & replace 'actions' to all fields that are listed in the 'fields' element of the arrays contained in '$markdownSearchReplaceActionsArray':
+				foreach ($markdownSearchReplaceActionsArray as $fieldActionsArray)
+					if (in_array($rowFieldName, $fieldActionsArray['fields']))
+						$row[$rowFieldName] = searchReplaceText($fieldActionsArray['actions'], $row[$rowFieldName], true); // function 'searchReplaceText()' is defined in 'include.inc.php'
+
+
+			// Order attributes according to the chosen output style & record type:
+			$record = citeRecord($row, $citeStyle, $citeType, $markupPatternsArray, false); // function 'citeRecord()' is defined in the citation style file given in '$citeStyleFile' (which, in turn, must reside in the 'cite' directory of the refbase root directory), see function 'generateCitations()'
+
+
+			// Print out the current record:
+			if (!empty($record)) // unless the record buffer is empty...
+			{
+				// Print any section heading(s):
+				if (preg_match("/year|type/i", $citeOrder))
+				{
+					$headingPrefix = "";
+					$headingSuffix = "";
+
+					if (!empty($headerMsg)) // if there's a custom header message available, we decrease the heading level of sections & subsections by one (since the header message has level 1)
+					{
+						$sectionMarkupPrefix = "## ";
+						$sectionMarkupSuffix = " ##\n\n";
+						$subSectionMarkupPrefix = "### ";
+						$subSectionMarkupSuffix = " ###\n\n";
+					}
+					else // no custom header message given
+					{
+						$sectionMarkupPrefix = "# ";
+						$sectionMarkupSuffix = " #\n\n";
+						$subSectionMarkupPrefix = "## ";
+						$subSectionMarkupSuffix = " ##\n\n";
+					}
+
+					list($yearsArray, $typeTitlesArray, $sectionHeading) = generateSectionHeading($yearsArray, $typeTitlesArray, $row, $citeOrder, $headingPrefix, $headingSuffix, $sectionMarkupPrefix, $sectionMarkupSuffix, $subSectionMarkupPrefix, $subSectionMarkupSuffix); // function 'generateSectionHeading()' is defined in 'cite.inc.php'
+
+					$markdownData .= $sectionHeading;
+				}
+
+				// Write plain TEXT paragraph:
+				$markdownData .= $record . "\n\n"; // create paragraph with encoded record text
+			}
+		}
+
+
+		return $markdownData;
+	}
+
+	// --- END CITATION FORMAT ---
+?>