Merge pull request #4 from civicrm/master

merge from core

README.md

-# CiviCRM developer documentation
+# CiviCRM Developer Guide
 
-```bash
-git clone https://github.com/civicrm/civicrm-dev-docs
-cd civicrm-dev-docs
-mkdocs serve
-```
+-   [Read published version](http://docs.civicrm.org/dev/en/master)
+-   [Learn how to edit](https://docs.civicrm.org/dev/en/master/documentation/#how-to-edit)
 
-This will likely be merged with the `civicrm-core` repo at some point.
-
-# See also
-
- * Download mkdocs: http://mkdocs.org/
- * Browse published dev docs: http://docs.civicrm.org/dev/en/master
- * Review general info about CiviCRM docs: https://github.com/civicrm/civicrm-docs
+This Developer Guide will likely be merged into the
+[civicrm-core](https://github.com/civicrm/civicrm-core/) repo at some point.
\ No newline at end of file

docs/extensions/advanced.md

+# Advanced patterns
+
+[]( FIXME remove this banner after review)
+>> NOTE: Some of these instruction maybe deprecated and superceded by better
+>> approaches.
+
+## Web Services
+
+There are three options to create an ajax or web-service callback:
+
+-   **Full control:**Add a basic page. Remove the parent::run() call
+    from the run() function, and at the bottom of the run() function,
+    perform your own output (eg "*echo json\_encode($data)*") and then
+    short-circuit processing (eg "*CRM\_Utils\_System::civiExit()*") so
+    that neither Smarty nor the CMS modify the output.
+-   **Using ajax helpers (CiviCRM 4.5 and above**): Generate a page with
+    civix as above. Build your data in the run() function. If the
+    client-side request includes *snippet=json* in the url, just append
+    your data to *$this-\>ajaxResponse* array and the rest will happen
+    automatically. If not, you can directly call
+    CRM\_Core\_Page\_AJAX::returnJsonResponse() at the bottom of the run
+    function. See [Ajax Pages and
+    Forms](/confluence/display/CRMDOC/Ajax+Pages+and+Forms)
+    documentation.
+-   **Using the API:** Add an API function using `civix`.
+    The API function can be called with the API's [AJAX
+    Interface](http://wiki.civicrm.org/confluence/display/CRMDOC/AJAX+Interface).
+    This automatically handles issues like encoding and decoding the
+    request/response.
+
+## Standalone PHP scripts
+
+Instead of creating a standalone script, consider one of these options:
+
+-   Add an API function (using the instructions above). The API function
+    can be called many different ways – cv, PHP, REST, AJAX, CLI, Drush,
+    Smarty, cron, etc. CiviCRM used to include a number of standalone
+    scripts – many of these have been migrated to API functions because
+    this approach is simpler and more flexible.
+-   Add a basic page (using the instructions above). At the bottom of
+    the run() function, call "*CRM\_Utils\_System::civiExit()*" to
+    short-circuit theming and CMS processing.
+
+Creating a pure standalone PHP script is a tricky proposition and likely to be
+brittle compared with the above.
+
+If the script is truly standalone and
+does not require any services from the CRM or CMS, then you can just add a
+new `.php` file to the extension... but it won't have access to CiviCRM's
+APIs, databases, classes, etc. If the standalone script needs those
+services, then it will need to ***bootstrap*** CiviCRM and the CMS. This
+is challenging for several reasons:
+
+-   The bootstrap mechanics are different in each CMS (Drupal, Joomla,
+    etc).
+-   The bootstrap mechanics are different for single-site installations
+    and multi-site installations
+-   To initiate a bootstrap from a script, one needs to determine the
+    local-path to the CiviCRM settings. However, the local-path of the
+    script is entirely independent of the local-path to the settings –
+    these are determined at the discretion of the site administrator.
+
+If you really need to do it, it's theoretically possibly to emulate an
+example like
+"[bin/deprecated/EmailProcessor.php](http://svn.civicrm.org/civicrm/branches/v4.1/bin/deprecated/EmailProcessor.php)".
+The results will likely be difficult for downstream users to
+install/use.
+
+
+## Cron jobs
+
+One can add an API function (using the instructions above) and create a
+schedule record. In CiviCRM 4.3, the schedule record can be
+automatically created; to do this, call "civix
+[generate:api](http://generateapi)" with the option "–schedule Daily"
+(or "-schedule Hourly", etc). CiviCRM will make a best-effort to meet
+the stated schedule.
+
+In CiviCRM 4.2, one can use APIs as cron jobs, but the schedule record
+won't be created automatically. The site administrator must manually
+insert a scheduling record by navigating to "Administer =\> System
+Settings =\> Scheduled Jobs".
+

docs/extensions/basics.md

@@ -14,8 +14,41 @@ This section covers how to write extensions. See the [extension life cycle
 page](/extend-stages) for background on the publishing and review process for
 [published extensions](https://civicrm.org/extensions).
 
+## Extension Names
+
+All extension names follow the same convention as Java package names – they
+look like reversed domain names. (e.g.  `com.example.myextension`). For
+module-extensions, the last word in the module name will be the module's
+*short-name*. The short-name *must* be unique. It is possible to pick a
+different short-name, but that requires extra work.
+
+## Pre-Requisites
+
+-   Have basic knowledge of PHP, Unix, and object-oriented programming
+-   Install ***civix v14.01*** or newer. For instructions, see
+    [https://github.com/totten/civix/](https://github.com/totten/civix/)
+    . This wiki page assumes that "civix" is installed and registered in
+    the PATH.
+-   Configure an extensions directory. For instructions, see
+    [Extensions](http://wiki.civicrm.org/confluence/display/CRMDOC/Extensions).
+    This wiki page assumes the directory is "/var/www/extensions", but
+    you should adapt as appropriate.
+     Your extensions directory must be under the CMS root directory so
+    that civix can find and bootstrap the CMS. Otherwise, it will fail
+    with an error like "Sorry, could not locate bootstrap.inc" on most
+    operations.
+-   The user account you use to develop the module must have permission
+    to read all CMS files, including configuration files, and write to
+    the extensions directory.
+     For example, Debian's drupal7 package saves database configuration
+    to /etc/drupal/7/sites/default/dbconfig.php, which is only readable
+    by the www-data user. You will need to make this file readable by
+    your development user account for civix to work.
+
 ## General overview
 
+[]( fixme paragraph this section into above notes )
+
 If you haven't already, you need to configure a local directory to store
 extensions.
 For instructions, see

docs/extensions/civix.md

-Coming soon!
+# Civix
+
+>> ![information](../img/info.png)
+Note: This page started
+[here in the wiki](https://wiki.civicrm.org/confluence/display/CRMDOC/Create+a+Module+Extension).
+We have not yet transferred all of the script snipets, so you may wish to
+peruse this page as well.
+
+## Introduction
+
+The [`civix`](https://github.com/totten/civix/) command-line tool is the
+community-endorsed method for building your CiviCRM extensions.
+
+Follow the installation instructions in the
+[GitHub repository](https://github.com/totten/civix/).
+
+In order to verify that all your configuration is correct ping CiviCRM from
+within your extensions directory with:
+
+```bash
+civix civicrm:ping
+```
+
+This command should reply with "Ping successful".
+If the ping is unsuccessful, re-read the civix README.md and do the
+post-installation configuration.
+
+It is also useful to examine the output of the `civix help` command to read
+about what `civix` can do for you.
+
+Help is available on individual commands, e.g.:
+
+```bash
+civix help civicrm:ping
+```
+
+## Generating a skeletal extension
+
+To generate a skeletal extension module, we will use `civix generate:module`
+and pass in the name for our extension. See [here](./basics/#extension-names)
+for details of naming conventions.
+
+Start with:
+
+```bash
+cd $YOUR_EXTENSIONS_DIR
+civix generate:module --help
+```
+
+Then use a command like this:
+
+```bash
+civix generate:module com.example.myextension --license=AGPL-3.0
+```
+
+This command will report that it has created three files, following the
+[standard extension structure](./files).
+
+The command attempts to autodetect authorship information (your name and
+email address) by reading your
+[`git`](https://git-scm.com/book/en/v2/Getting-Started-First-Time-Git-Setup)
+configuration. If this fails or is
+otherwise incorrect, then you may pass explicit values with `--author`
+and `--email`.
+
+You can now update your `info.xml`. This file initially contains some
+examples and placeholders which you need to fix. You can edit most of these
+fields intuitively.  If you need detailed specifications, see [Extension
+Reference](http://wiki.civicrm.org/confluence/display/CRMDOC/Extension+Reference).
+
+Now that you have created your extension, you need to activate it by navigating
+to:
+
+**Administer » System Settings » Manage Extensions**
+
+or
+
+**Administer » Customize Data and Screens » Manage Extensions.**
+
+For more detailed instructions, see
+[Extensions](http://wiki.civicrm.org/confluence/display/CRMDOC/Extensions).
+
+## Add features
+
+There are many different features that you can add to a module-extension
+at your discretion. A few possibilities:
+
+### Add a basic web page
+
+CiviCRM uses a typical web-MVC architecture. To implement a basic web
+page, you must create a PHP controller class, create a Smarty template
+file, and create a routing rule. You can create the appropriate files by
+calling "civix generate:page"
+
+Once again you can review the output of this command to see the available options:
+
+```bash
+civix generate:page --help
+```
+
+Generally you will only need to supply the PHP class name and web-path,
+for example:
+
+```bash
+civix generate:page MyPage civicrm/my-page
+```
+
+This creates three files:
+
+-   `xml/Menu/myextension.xml` defines request-routing rules and
+    associates the controller ("CRM\_Myextension\_Page\_Greeter") with
+    the web path ("civicrm/my-page")
+-   `CRM/Myextension/Page/MyPage.php` is the controller which
+    coordinates any parsing, validation, business-logic, or database
+    operations.
+-   `templates/CRM/Myextension/Page/MyPage.tpl` is loaded
+    automatically after the controller executes. It defines the markup
+    that is eventually displayed. For more information on the syntax of
+    this file, see
+    [the smarty guide](http://www.smarty.net/docsv2/en/).
+
+The auto-generated code for the controller and view demonstrate a few
+basic operations, such as passing data from the controller to the view.
+
+>> ![information](../img/info.png)
+After adding or modifying a route in the XML file, you must reset
+CiviCRMs "menu cache". Do this in a web browser by visiting
+"/civicrm/menu/rebuild?reset=1" or by running
+`drush cc civicrm` if using Drupal & Drush.
+
+**Edit In Place**
+
+If the data on the page is read and updated through the API, then you
+may want to consider using the [in-place
+editing](/confluence/display/CRMDOC/In-Place+Field+Editing) API.
+
+### Add a basic web form
+
+>> ![danger](../img/danger.png)
+The form system is not well documented and may undergo significant
+revision after the CiviCRM 4.x series. In general, migrating basic pages
+will be easier than migrating basic forms, so you may want
+to consider building your data-input interface  using basic pages, the AJAX API,
+and the
+[in-place editing](/confluence/display/CRMDOC/In-Place+Field+Editing) API.
+
+CiviCRM uses a typical web-MVC architecture. To implement a basic web
+form, you must create a PHP controller class, create a Smarty template
+file, and create a routing rule. You can create the appropriate files by
+calling "civix generate:form".
+
+The form generation command has similar arguments to `civix generate:page`,
+requiring a class name and a web route:
+
+```bash
+civix generate:form FavoriteColor civicrm/favcolor
+```
+
+This creates three files:
+
+-   `xml/Menu/myextension.xml` defines request-routing rules and
+    associates the controller ("CRM\_Myextension\_Form\_FavoriteColor")
+    with the web path ("civicrm/favcolor")
+-   `CRM/Myextension/Form/FavoriteColor.php` is the controller which
+    coordinates any parsing, validation, business-logic, or database
+    operations. For more details on how this class works, see [QuickForm
+    Reference](http://wiki.civicrm.org/confluence/display/CRMDOC/QuickForm+Reference).
+-   `templates/CRM/Myextension/Form/FavoriteColor.tpl` is loaded
+    automatically after the controller executes. It defines the markup
+    that is eventually displayed. For more information on the syntax of
+    this file, see
+    [the smarty guide](http://www.smarty.net/docsv2/en/).
+
+The auto-generated code for the controller and view demonstrate a few
+basic operations, such as adding a <SELECT\> element to the form.
+
+>> ![information](../img/info.png)
+After adding or modifying a route in the XML file, you must reset
+CiviCRMs "menu cache". This can be done in a web browser by visiting
+"/civicrm/menu/rebuild?reset=1"
+
+### Add a database upgrader, installer and uninstaller
+
+If your module requires creating or maintaining SQL tables, then you
+should create a class for managing database upgrades. The upgrader adds
+a class for managing installs and upgrades but you then need to edit the file
+comment out the various upgrade and uninstall functions
+to make it work. Generally your install script belongs in an `sql/` folder
+in the root of your extension with a name like 'install'
+
+This `civix` command does not require arguements:
+
+```bash
+civix generate:upgrader
+```
+
+This creates two files and one directory:
+
+-   `CRM/Myextension/Upgrader.php` stores a series of upgrade
+    functions based on a function naming pattern similar to
+    Drupal's
+    [hook\_update\_N](http://api.drupal.org/api/drupal/modules%21system%21system.api.php/function/hook_update_N/7).
+    After examining the file's comments for example upgrade functions
+    you can then write your own.
+-   `CRM/Myextension/Upgrader/Base.php` contains helper functions
+    and adapters which make it easier to write the upgrader. This file
+    may be overwritten from time-to-time to provide new helpers or
+    adapters.
+-   sql
+
+After reviewing the examples and creating your own upgrade functions,
+you can execute the upgrades through the web interface by visiting the
+"Manage Extensions" screen. This screen will display an alert with an
+action-link to perform the upgrades.
+
+>> ![information](../img/info.png)
+The "upgrader" class is a wrapper for
+[hook\_civicrm\_upgrade](/confluence/display/CRMDOC43/Hook+Reference)
+which aims to be easy-to-use for developers with Drupal experience. If
+you need to organize the upgrade logic differently, then consider
+providing your own implementation of hook\_civicrm\_upgrade.
+
+>> ![danger](../img/danger.png)
+Only use the upgrade system to manage new SQL
+tables. Do not manipulate core schema.
+
+If you need to create triggers on core SQL tables, use
+[hook\_civicrm\_triggerInfo](http://wiki.civicrm.org/confluence/display/CRMDOC/Hook+Reference).
+This allows your triggers to coexist with triggers from other modules.
+
+### Add a case type
+*(from CiviCRM v4.4+)*
+
+If you want to develop a custom case-type for CiviCase, then you can
+generate a skeletal CiviCase XML file.
+
+Once again `civix` will give the details of options and arguments with this
+command:
+
+```bash
+civix help generate:case-type
+```
+
+This reports that civix expects a <Label> argurment and an optional name:
+
+```bash
+civix generate:case-type "Volunteer Training" Training
+```
+
+This creates two files:
+
+-   `xml/case/Training.xml` defines the roles, activity types, and
+    timelines associated with the new case type. For more in depth
+    discussion of CiviCase XML, see [CiviCase
+    Configuration](/confluence/display/CRMDOC/CiviCase+Configuration).
+-   `alltypes.civix.php`(which may already exist) defines
+    implementations of various hooks (notably hook\_civicrm\_caseTypes).
+
+### Add custom fields
+*(from CiviCRM v4.4+)*
+
+Your extension can create one or more sets of custom
+fields at installation. There are two
+methods depending on whether the custom data set extends an entity
+(e.g. "Individual" – without any specific subtype)
+or exends a specific subtype of an entity.
+(e.g. Activities of type 'Volunteer')
+
+#### Extending a base entity
+
+This is the simplest scenario.
+Start by creating a custom fields using the web interface and then export
+them for use with the extension:
+
+>> ![information](../img/info.png)
+Before you begin verify that civix is connected to your instance of CiviCRM by running `civix civicrm:ping`.
+
+-   On your development instance of CiviCRM, create the new custom
+    fields using the web interface. Note the unique ID of the custom data
+    group (also known as the "Custom Fieldset", "CustomGroup" or
+    "civicrm\_custom\_group")
+-   Create an XML file with `civix generate:custom-xml`
+    specifying the custom-data group ID.
+-   Create an upgrader file with `civix generate:upgrader` to
+    load the XML file during installation.
+
+Check the full range of options with the `civix` help command:
+
+```bash
+civix help generate:custom-xml
+```
+
+So to created your XML for a custom data group ID of 7:
+
+```bash
+civix generate:custom-xml --data=7
+```
+
+Most of the [CiviHR](https://github.com/civicrm/civihr/tree/master) modules rely on the first approach (e.g.:
+[Upgrader/Base.php](https://github.com/civicrm/civihr/blob/master/hrqual/CRM/HRQual/Upgrader/Base.php#L244) and
+[auto\_install.xml](https://github.com/civicrm/civihr/blob/master/hrqual/xml/auto_install.xml)).
+
+#### Extending an subtype
+
+<!-- This section still is not really clear to me.
+Is this really about sub-types in an OO sense?? or subtypes in as a base
+entity of a particular type as defined by its properties?
+-->
+
+The automatic export does not work too well when the
+custom-data group extends a specific subtype. The
+"HR Emergency Contact" extension provides and example that creates
+a custom-data group that describes
+Relationships with type "Emergency Contact". Internally, Civi uses
+"relationship type IDs", but those are not portable. As a quick
+work-around, this extension uses Smarty:
+([HREmerg/Upgrader.php](https://github.com/civicrm/civihr/blob/master/hremerg/CRM/HREmerg/Upgrader.php#L14)
+and
+[hremerg-customdata.xml.tpl](https://github.com/civicrm/civihr/blob/master/hremerg/templates/hremerg-customdata.xml.tpl#L11)).
+
+To create this extension, the author used `civix generate:custom-data` and
+then:
+
+1. Renamed the `xml/auto\_install.xml` to
+ `templates/hremerg-customdata.xml.tpl`
+2. Changed the value of `<extends\_entity\_column\_value\>` in the
+  `.tpl file` using  a variable instead of a hard-coded type ID.
+3. Added logic in the upgrader to create the relationship type
+4. Added logic in the upgrader to evaluate the Smarty template
+
+### Add a hook function
+
+CiviCRM
+[hook functions](http://wiki.civicrm.org/confluence/display/CRMDOC/Hook+Reference)
+allow extensions to run extra logic as
+part of the normal CiviCRM processing. For example,
+`hook\_civicrm\_buildForm()` allows a module to run logic whenever a
+web-form is displayed, and `hook\_civicrm\_post()` allows a module to
+run logic after any entity is saved.
+
+Hook function names follow the Drupal convention of being
+the module's short-name concatenated to the hook name. This strict but simple
+naming convention is what allows the CiviCRM core to locate your hook
+functions and call them at the appropriate times.
+For example, if our module's main file is
+`myextension.php` and we want to use `hook\_civicrm\_post()`
+to write to a log file every time a contribution is saved, then our function must be called `myextension_civicrm_post()`:
+
+To implement a hook, add a function to the module's main `.php`
+file created earlier with `civix generate:module`:
+
+```php
+/**
+ * Implementation of hook_civicrm_post
+ */
+function myextension_civicrm_post($op, $objectName, $objectId, &$objectRef) {
+  switch ($objectName) {
+    case 'Contribution':
+      $file = '/tmp/contributions.log';
+      $message = strtr("Performed \"@op\" at @time on contribution #@id\n", array(
+        '@op' => $op,
+        '@time' => date('Y-m-d H:i:s'),
+        '@id' => $objectId,
+      ));
+      file_put_contents($file, $message, FILE_APPEND);
+      break;
+    default:
+      // nothing to do
+  }
+}
+```
+
+>> ![information](../img/info.png)
+When you first created the skeletal project, several hook functions were
+auto-generated in `myextension.php`. These functions are usually about
+one line long – they simply delegate the work to another function. For
+example `myextension\_civicrm\_config()` delegates work to
+`\_myextension\_civix\_civicrm\_config()`. You should feel free to add
+more code to `myextension\_civicrm\_config()`, but you should preserve
+the call to `\_myextension\_civix\_civicrm\_config()`. <!-- fixme! why?? -->
+
+### Add a resource file
+
+To include static resources such as stylesheets, Javascript files, or
+images place them in your extension directory. To load
+the files at runtime, see the examples in the [Resource
+Reference](http://wiki.civicrm.org/confluence/display/CRMDOC/Resource+Reference).
+
+### Add a report
+
+CiviReport enables developers to define new business reports using
+customizable SQL logic and form layouts.
+If another existing report is close to your needs you may copy and modify it.
+
+To to see the available report generation options acitivate the `civix` help:
+
+```bash
+civix generate:report --help
+```
+
+To create a new report specify the report PHP class name and the CiviCRM component, for example:
+
+```bash
+civix generate:report MyReport CiviContribute
+```
+
+This creates three files:
+
+-   `CRM/Myextension/Form/Report/MyReport.mgd.php` stores metadata
+    about the report in a format based on
+    [hook\_civicrm\_managed](http://wiki.civicrm.org/confluence/display/CRMDOC/Hook+Reference)
+    and the
+    [API](http://wiki.civicrm.org/confluence/display/CRMDOC/API+Reference).
+-   `CRM/Myextension/Form/Report/MyReport.php` contains the
+    form-builder and query-builder for the report. For details about its
+    structure, see the [CiviReport
+    Reference](http://wiki.civicrm.org/confluence/display/CRMDOC/CiviReport+Reference).
+-   `templates/CRM/Myextension/Form/Report/MyReport.tpl` contains
+    the report's HTML template. This template usually delegates
+    responsibility to a core template and does not need to be edited.
+
+If one of the existing reports is close to meeting
+your needs, but requires further PHP or SQL customization, you may
+simply make a new report based on that report.
+To copy a report, find the class-name of the original report within the
+`civicrm/CRM/Report/Form/` directory in the CiviCRM repository.
+Then run the `civix generate:report` command using the copy option
+from with your extension directory.
+
+For example, this command will copy the activity report in the class
+`CRM\_Report\_Form\_Activity` to a new report within your extension:
+
+```bash
+civix generate:report --copy CRM_Report_Form_Activity MyActivity Contact
+```
+
+### Add a custom search
+
+CiviCRM enables developers to define new search forms using customizable
+SQL logic and form layouts. Use this command to get started:
+
+```bash
+civix help generate:search
+```
+
+Then you could generate your basic search code for a MySearch class with:
+
+```bash
+civix generate:search MySearch
+```
+
+This command will create two files:
+
+-   `CRM/Myextension/Form/Search/MySearch.mgd.php` stores metadata
+    about the custom search. The format of the file is based on
+    [hook\_civicrm\_managed](http://wiki.civicrm.org/confluence/display/CRMDOC/Hook+Reference)
+    and the
+    [API](http://wiki.civicrm.org/confluence/display/CRMDOC/API+Reference).
+-   `CRM/Myextension/Form/Search/MySearch.php` contains the
+    form-builder and query-builder for the custom search.
+
+
+If one of the existing searches is close to
+meeting your needs you may copy it instead and then customise the
+PHP, SQL and templates.
+
+To make a new search based on an existing search first determine the name of
+the original search class within the `civicrm/CRM/Contact/Form/Search/Custom`
+directory of CiviCRM source tree. Then run the "generate:search" command from
+within your module directory.
+
+For example, the zipcode search is in the class
+`CRM\_Contact\_Form\_Search\_Custom\_ZipCodeRange`, so you can copy it with:
+
+```bash
+civix generate:search --copy CRM_Contact_Form_Search_Custom_ZipCodeRange MySearch
+```
+
+The "copy" option will create either two or three files depending
+on whether the original search screen defines its own Smarty template.
+
+### Add an API function
+
+The [CiviCRM API](../api/general)
+provides a way to expose functions for use by other developers. API
+functions allow implementing AJAX interfaces (using the
+cj().crmAPI() helper), and they can also be called via REST, PHP,
+Smarty, Drush CLI, and more. Each API requires a two-part name: an
+entity name (such as "Contact", "Event", or "MyEntity") and an action
+name (such as "Create" or "MyAction").
+
+Get started by accessing the `civix` help:
+
+```bash
+civix help generate:api
+```
+
+>> ![information](../img/info.png)
+Action names must be lowercase. The javascript helpers `CRM.api()` and
+`CRM.api3()` force actions to be lowercase. This issues does not present
+itself in the API Explorer or when the api action is called via PHP,
+REST, or SMARTY.
+
+You can make your API code with a command in this pattern:
+
+```bash
+civix generate:api NewEntity NewAction
+```
+
+This creates one file:
+
+-   `api/v3/NewEntity/NewAction.php` provides the API function.
+    that the parameters and return values must be processed in a
+    particular way (as demonstrated by the auto-generated file).
+
+<!-- fixme - clarify is this 4.3 and later? -->
+For use with CiviCRM 4.3, you can also add the "–schedule" option (e.g.
+"–schedule Hourly"). This will create another file:
+
+-   `api/v3/NewEntity/NewAction.mgd.php` provides the scheduling
+    record that will appear in the CiviCRM's job-manager.
+
+### Add a new entity
+
+>> ![danger](../img/danger.png)
+This functionality is considered "experimental and incomplete".
+
+You may have a need to create a new entity that does not exist in
+CiviCRM. For this, you can use the command `civix generate:entity`
+
+-   Pick a name for your entity. In some places, CiviCRM expects a
+    *FirstLetterCapitalizedName*, in others, an *underscore\_name*. Be
+    absolutely consistent in your naming, because CiviCRM needs to
+    translate between those two naming conventions.
+
+-   Run `civix generate:entity <name of entity>` (entity name should be
+    FirstLetterCapitalized here). This creates a skeletal file for your
+    XML schema, your BAO, and your API. It does NOT create a skeletal
+    SQL file to create your table or DAO files at this time.
+-   Edit the XML schema in the "xml" folder to match the fields you
+    want. Minimal documentation is available
+    [here](https://wiki.civicrm.org/confluence/display/CRMDOC/Database+Reference),
+    but you are better off looking at the [existing XML
+    schemata](https://github.com/civicrm/civicrm-core/tree/master/xml/schema).
+-   Create a DAO file. For now, civix does not handle this. You can
+    create this by hand. Alternatively, use [this
+    technique](http://civicrm.stackexchange.com/a/3536/12). Copy your
+    XML schema into a development copy of CiviCRM. Edit Schema.xml to
+    include your XML file, then from the xml folder, run
+    `php ./GenCode.php` (In CiviCRM 4.7.12+, run
+    `<civiroot>/bin/setup.sh -g` instead). This will generate a DAO file
+    for you in the CiviCRM core code; copy it into the
+    CRM/<Entityname\>/DAO folder of your extension.
+-   Currently, `civix` does not generate the SQL to create and
+    drop your table(s). You can create these by hand, or, if
+    you used the `<civiroot>/bin/setup.sh -g` technique to create your
+    DAO, SQL will have been generated for you in
+    `<civiroot>/sql/civicrm.mysql`. Once you have the SQL statements for
+    creating and dropping your SQL tables, create
+    `auto_install.sql` and `auto_uninstall.sql`
+    respectively in your 'sql/' folder. CiviCRM will run them
+    automatically on install if you generated an upgrader. Note that
+    using `auto_install.sql` and `auto_uninstall.sql`
+    is not best practice if you have multiple statements in each file,
+    since you cannot error check each statement separately.
+    <!-- fixme update and clarify -->
+-   Run `civix generate:upgrader` from within your extension.
+-   Define your entity using
+    [hook\_civicrm\_entityTypes](https://wiki.civicrm.org/confluence/display/CRMDOC/hook_civicrm_entityTypes).
+
+### Add a unit-test class
+
+Unit-testing is essential to maintain quality-control over
+your extension. When developing a test case for a CiviCRM extension, it
+is useful to run the test case within an active, clean CiviCRM
+environment. The combined CiviCRM `civix` testing tools will automate this as
+long as you follow a few basic conventions.
+
+The following steps will create and run a test in your extension.
+
+>> ![information](../img/info.png)
+Before preparing unit-tests with extensions, you must first
+[configure you personal testing sandbox](/confluence/display/CRM/Setting+up+your+personal+testing+sandbox+HOWTO) and enable your extension on the sandbox.
+
+Explore the full options with:
+
+```bash
+civix help generate:test
+```
+
+To create a skeletal test-class choose a class name in
+your extension's namespace (*CRM\_Myextension*) that ends with the
+word *Test*:
+
+```bash
+civix generate:test CRM_Myextension_MyTest
+```
+
+This creates a new directory and a new PHP file:
+
+-   `tests/phpunit` is the base directory for all test classes.
+-   `tests/phpunit/CRM/Myextension/MyTest.php` is the actual test
+    class. It should be written according to the conventions of
+    [PHPUnit](http://www.phpunit.de/manual/current/en/writing-tests-for-phpunit.html).
+
+To make sure you can run the test civix needs to know where the CiviCRM
+base install is:
+
+The skeletal test class does not do anything useful. For more details on
+how to write a test class:
+
+-   Read [PHP Unit Manual: Writing Tests for
+    PHPUnit.](https://phpunit.de/manual/current/en/writing-tests-for-phpunit.html)
+-   Review the example code in
+    [org.civicrm.exampletests](https://github.com/totten/org.civicrm.exampletests)
+
+>> ![danger](../img/danger.png)
+The following instructions are deprecated. Updated instructions coming soon.
+
+```bash
+# Check if civix can connect to the civi api
+civix civicrm:ping
+# Look at your current config
+civix config:get
+# Tell civix where to read the civicrm.settings.php
+# EG. For Drupal
+civix config:set civicrm_api3_conf_path /your/path/to/sites/default
+```
+
+To run this test-class, change to your extension folder and call "civix
+test":
+
+```bash
+civix test CRM_Myextension_MyTest
+```
+

docs/extensions/files.md

-Coming soon!
+# Extension files
+
+The [civix](./civix) command line tool will generate the following structure
+for you:
+
+-   ***info.xml*** is a manifest that describes your extension – the
+    name, license, version number, etc. You should edit most information
+    in this file.
+-   ***myextension.php*** stores source code for all your hooks. It
+    includes a few default hook implementations which will make
+    development easier. You can add and remove hooks as you wish. (Note:
+    This file name is different in each module – it is based the
+    module's *[short-name](./basics/#extension-names)*.)
+-   ***myextension.civix.php*** contains auto-generated helper
+    functions. These deal with common problems like registering your
+    module in the template include-path. `civix` may automatically
+    overwrite this file, so generally do not edit it.
+
+In addition, it creates some empty directories. These directories are
+reminiscent of the directory structure in CiviCRM core:
+
+-   ***CRM/Myextension/*** stores PHP class files. Classes in this
+    folder should be prefixed with "CRM\_Myextension\_"
+-   ***templates/*** stores Smarty templates
+-   ***xml/*** stores XML configuration files (such as URL routes)
+-   ***build/*** stores exportable .zip files

docs/extensions/troubleshooting.md

+# Troubleshooting
+
+If you are struggling, the best thing to do is reach out to the
+[CiviCRM community](../basics/community).
+
+If you cannot find the answer in this guide or by searching in the
+[CiviCRM StackExchange site](http://civicrm.stackexchange.com/)
+then please [ask](http://civicrm.stackexchange.com/questions/ask). Asking
+questions on StackExchange not only helps you but may well help others who
+follow you.
+
+That said, this is a small list of some of the commoner problems extension
+writers encounter.
+
+## Extension not doing anything
+
+[]( ###### arguably this list should be removed altogether?? #### )
+
+Q: I've created the files and edited them but I don't see the expected
+changes.
+
+A: Did you install and enable your extension?
+(<site\>/civicrm/admin/extensions?reset=1)
+
+## Civix error messages
+
+Q: I get Error: "Cannot instantiate API client -- please set connection
+options in parameters.yml"
+
+A: You might have missed the step about setting
+'civicrm\_api3\_conf\_path'
+([https://github.com/totten/civix/](https://github.com/totten/civix/)),
+or it didn't get set properly for some reason.
+
+Q: I've tried to generate a page/report/search/upgrader/etc with civix
+but it's not working.
+
+A: For all of the various types, you must first run
+[generate:module](http://generatemodule), and then \`cd\` into the
+folder (e.g. com.example.myextension) before running one of the
+other \`generate:\` commands.
+

docs/index.md

 # CiviCRM Developer Guide
 
+!!! warning "Notice"
+    This guide is not yet complete.
+    As of early 2017 we are actively working to migrate content in from the
+    [wiki]. Read more about this [migration process][migration], including how
+    to help out!
+
+[wiki]: http://wiki.civicrm.org/confluence/display/CRMDOC/Develop
+[migration]: https://wiki.civicrm.org/confluence/display/CRMDOC/Content+migration+from+wiki+to+Developer+Guide
+
+
 [CiviCRM](https://civicrm.org) is an open-source application. The code can be
 poked, prodded, twisted, and hacked. It can be customized, extended, and
 collaboratively developed. This documentation tells you how to do that.
@@ -23,39 +33,4 @@ for use by people that are familiar with CiviCRM development.
     for specific details on editing this documentation (and others using
     mkdocs). You can also learn how to read these docs off-line!
 
-## Migration of content is in progress
-
-As of early 2017 we are actively working to migrate content from the [wiki] to
-this guide. Read more about this [migration process][migration], including how
-to help out!
-
-[wiki]: http://wiki.civicrm.org/confluence/display/CRMDOC/Develop
-[migration]: https://wiki.civicrm.org/confluence/display/CRMDOC/Content+migration+from+wiki+to+Developer+Guide
-
-## Other sources of information
-
-As an open-source project, CiviCRM is managed by an international community of
-developers and activists. Help from these people can be found in the following
-ways:
-
--   Our [chat rooms](https://chat.civicrm.org/) and
-    [mailing lists](http://lists.civicrm.org/lists/info/civicrm-dev) are great
-    places to say hello and discuss CiviCRM issues with others.
-
--   If you need help, your best bet is probably our
-    [stack exchange Q+A site](http://civicrm.stackexchange.com/).
-
--   If you've identified a problem, you can file issues on our
-    [issue](http://issues.civicrm.org/) on our issue tracker or fix the issue
-    and submit a pull request on
-    [Github](https://github.com/civicrm/civicrm-core/).
-
--   If you've written an extension, please share it in our
-    [extensions directory](https://civicrm.org).
-
--   Use the [wiki](http://wiki.civicrm.org/confluence/display/CRM/CiviCRM+Wiki)
-    to share drafts, notes, and specs.
 
--   And don't forget you are always welcome to come to a
-    [real world event](https://civicrm.org/events) like a conference meet-up
-    or sprint.

docs/js/custom.js

+$(function() {
+
+  // Automatically scroll the navigation menu to the active element
+  //   https://github.com/civicrm/civicrm-dev-docs/issues/21
+  $.fn.isFullyWithinViewport = function(){
+      var viewport = {};
+      viewport.top = $(window).scrollTop();
+      viewport.bottom = viewport.top + $(window).height();
+      var bounds = {};
+      bounds.top = this.offset().top;
+      bounds.bottom = bounds.top + this.outerHeight();
+      return ( ! (
+        (bounds.top <= viewport.top) ||
+        (bounds.bottom >= viewport.bottom)
+      ) );
+  };
+  if( !$('li.toctree-l1.current').isFullyWithinViewport() ) {
+    $('.wy-nav-side')
+      .scrollTop(
+        $('li.toctree-l1.current').offset().top -
+        $('.wy-nav-side').offset().top -
+        60
+      );
+  }
+
+});

docs/markdownrules.md

@@ -32,10 +32,17 @@ platforms.
 
 ## Hyperlinks
 
--   A basic hyperlink
+-   A basic hyperlink (in a sentence)
 
         Try [CiviCRM](https://civicrm.org) for your database.
 
+-   An internal hyperlink on mkdocs (4 different ways that all work)
+
+        [extensions](/extensions/basics)
+        [extensions](/extensions/basics.md)
+        [extensions](extensions/basics)
+        [extensions](extensions/basics.md)
+
 -   With long URLs, the following syntax is better.
 
         See [this issue][CRM-19799] for more details.
@@ -85,7 +92,10 @@ This is a second.
 #### Heading 4
 ```
 
-Alternate syntax (only works for h1 and h2):
+The above syntax is [called](http://pandoc.org/MANUAL.html#headers)
+"ATX style headers" in markdown terminology, and is preferred my most.
+An alternate syntax called "setext style headers" works for h1 and h2 as
+follows:
 
 ```md
 Heading 1
@@ -272,7 +282,43 @@ mkdocs**:
 -   More list items
 ````
 
+## Admonitions
+
+### Types
+
+!!! note
+    I am a "note" admonition.
+
+!!! tip
+    I am a "tip" admonition.
+
+!!! warning
+    I am a "warning" admonition.
+
+!!! danger
+    I am a "danger" admonition.
+
+Other types
+
+-   "hint", "important" (visually identical to "tip")
+-   "attention", "caution" (visually identical to "warning")
+-   "error" (visually identical to "danger")
 
+### Syntax
+
+Simple example:
+
+```md
+!!! note
+    This feature is only available as of CiviCRM 4.5.
+```
+
+Add a custom title (make sure to quote the title):
+
+```md
+!!! danger "Don't try this at home!"
+    Stand back. I'm about to try science!
+```
 
 ## Images
 

mkdocs.yml

@@ -3,6 +3,10 @@ repo_url: https://github.com/civicrm/civicrm-dev-docs
 site_description: A guide for CiviCRM developers.
 site_author: The CiviCRM community
 theme: readthedocs
+extra_javascript:
+  - js/custom.js
+markdown_extensions:
+  - markdown.extensions.admonition
 pages:
 - Home: index.md
 - Basics:
@@ -25,8 +29,10 @@ pages:
    - All Available Hooks: hooks-db.md
 - Writing Extensions:
   - Basics: extensions/basics.md
-  # - civix: extensions/civix.md
-  # - Anatomy of Files: extensions/files.md
+  - Using civix: extensions/civix.md
+  - Anatomy of Files: extensions/files.md
+  - Advanced Patterns: extensions/advanced.md
+  - Troubleshooting: extensions/troubleshooting.md
   # - Using hooks: extensions/using-hooks.md
   # - Customizing Screens: extensions/customize-screens.md
   # - Creating Pages: Forms/extensions/create-page.md