Update links

Author: Jakob Jünger

docs/devel/backend/controller.md

@@ -7,8 +7,8 @@ Epigraf maps URLs to action methods in controller classes.
 These methods perform three primary functions:
 
 1. Parameter parsing: Extract and validate URL parameters that control the data retrieval and view rendering.
-2. Data Handling: Retrieve and store data using the [model](devel/backend/model) based on URL parameters and posted payloads.
-3. View Rendering: Pass data to [views](devel/backend/view) for the browser (HTML) or API responses (e.g. JSON).
+2. Data Handling: Retrieve and store data using the [model](/epigraf/devel/backend/model) based on URL parameters and posted payloads.
+3. View Rendering: Pass data to [views](/epigraf/devel/backend/view) for the browser (HTML) or API responses (e.g. JSON).
 
 ## URL Mapping and Routing
 
@@ -180,7 +180,7 @@ User settings in Epigraf are either stored in the user record or in the session.
 All controllers extend the `AppController` class (`src/Controller/AppController.php`)
 which is derived from the base `Controller` class provided by the CakePHP framework.
 
-![Application controller class hierarchy](devel/assets/img/classes-controller-app.png)
+![Application controller class hierarchy](/epigraf/devel/assets/img/classes-controller-app.png)
 
 On the application level, controllers serve the following purposes:
 
@@ -199,7 +199,7 @@ The Epi plugin implements an own `Epi\AppController` class (`plugins/Epi/Control
 derived from the global AppController, adding functionality for project database handling.
 All project database controllers within the Epi plugin extend this class.
 
-![Epi plugin controller class hierarchy](devel/assets/img/classes-controller-epi.png)
+![Epi plugin controller class hierarchy](/epigraf/devel/assets/img/classes-controller-epi.png)
 
 They Epi plugin controllers serve the following purposes:
 

docs/devel/backend/model.md

@@ -30,7 +30,7 @@ All Tables are derived from `src/Model/Table/BaseTable.php` and all Entities fro
 Common methods in the table classes are `findHasParams()` and `findContainFields()`
 which are used by the controllers to filter and retrieve data from the database based on query parameters.
 
-![Model class hierarchy (App)](devel/assets/img/classes-model-app.png)
+![Model class hierarchy (App)](/epigraf/devel/assets/img/classes-model-app.png)
 
 There are some pecularities in the models. You may need to read the section about project database models
 to understand the full picture:
@@ -64,7 +64,7 @@ Tables classes are usually derived from `plugins/Epi/src/Model/Table/BaseTable.p
 and entity classes from `plugins/Epi/src/Model/Entity/BaseEntity.php`.
 Both project database level base classes extend the corresponding application's base classes.
 
-![Model class hierarchy (Epi)](devel/assets/img/classes-model-epi.png)
+![Model class hierarchy (Epi)](/epigraf/devel/assets/img/classes-model-epi.png)
 
 Some special cases have to be considered:
 

docs/devel/backend/view.md

@@ -13,7 +13,7 @@ different view classes are used.
                The ApiView based classes are also used in the export pipelines
                to generate TEI-documents and other structured data formats.
 
-![View class hierarchy](devel/assets/img/classes-view.png)
+![View class hierarchy](/epigraf/devel/assets/img/classes-view.png)
 
 
 ## Rendering HTML for the Browser

docs/devel/database/datamodel.md

@@ -11,11 +11,11 @@ The tables include:
 - *databanks*: The configured project databases.
 - *users*: User data, including contact information and settings
 - *permissions*: User permissions,
-  see [Authentication and authorization](devel/backend/controller/#authentication-and-authorization).
+  see [Authentication and authorization](/epigraf/devel/backend/controller/#authentication-and-authorization).
 - *files*: Metadata for files managed by Epigraf.
 - *docs*: Wiki, help and public pages.
 - *pipelines*: Export pipeline configurations.
-- *jobs*: Each [batch operation](devel/database/batch-operations) generates a job.
+- *jobs*: Each [batch operation](/epigraf/devel/database/batch-operations) generates a job.
 
 See the entity classes in `src/model/Entity` for further information about the available fields in each table.
 
@@ -49,7 +49,7 @@ which includes the following tables:
 See below and see the entity classes in `plugins/Epi/src/model/Entity` for further information
 about the available fields in each table.
 
-![Graphic illustration of the data model](devel/assets/img/epigraf-data-model.png)
+![Graphic illustration of the data model](/epigraf/devel/assets/img/epigraf-data-model.png)
 
 ## Structure of the Project Databases
 

docs/devel/frontend/index.md

@@ -13,4 +13,4 @@ For interactive trees, tables and other widgets, Epigraf implements an own EpiWi
 Bundling JavaScript files, CSS files, language resources and images is done using Webpack.
 All bundles can be generated at once by calling `npm run build`.
 
-![Epigraf Editor](devel/assets/img/epigraf-editor.png)
+![Epigraf Editor](/epigraf/devel/assets/img/epigraf-editor.png)

docs/devel/frontend/templates.md

@@ -118,4 +118,4 @@ The application object implements methods...
 
 The `App` object is expanded by functions in widgets.js
 that attach JavaScript classes to HTML elements.
-See the [widget documentation](devel/frontend/widgets).
+See the [widget documentation](/epigraf/devel/frontend/widgets).

docs/devel/frontend/widgets.md

@@ -4,7 +4,7 @@ permalink: 'devel/frontend/widgets/'
 ---
 
 Epigraf uses a widget system to connect HTML elements with JavaScript classes.
-The widget HTML elements are generated in the [backend](devel/backend/view) by helper classes derived from CakePHP helpers.
+The widget HTML elements are generated in the [backend](/epigraf/devel/backend/view) by helper classes derived from CakePHP helpers.
 
 Each JavaScript widget class registers a CSS class and the framework instantiates and attaches the widget classes
 to the found elements. For example, a table with the class `widget-table` is supplemented by a `TableWidget` class.
@@ -31,7 +31,7 @@ The base classes of the framework are defined in `htdocs/js/base.js`:
   A document consists of several parts such as sections, footnotes and notes.
   Document classes hold together the different parts and manage the interaction between them.
 
-![Inheritance hierarchy](devel/assets/img/classes-widget-basemodel.png)
+![Inheritance hierarchy](/epigraf/devel/assets/img/classes-widget-basemodel.png)
 
 ### The Widget Life Cycle
 
@@ -127,7 +127,7 @@ Frames are HTML elements attached to derivates of the `BaseFrame` class that han
 - `TabFrame`: Responsible for tab sheets within in sidebars.
 - `PopupWindow`: Responsible for popups and dialogs.
 
-![Inheritance hierarchy](devel/assets/img/classes-widget-baseframe.png)
+![Inheritance hierarchy](/epigraf/devel/assets/img/classes-widget-baseframe.png)
 
 The frame classes handle dynamic content loading and trigger the respective widget lifecycle methods:
 - `loadElement()` displays a DOM element already constructed on the page.
@@ -162,7 +162,7 @@ Layout widgets provide extended functionality for the page layout (see `layout.j
 ## Collections: Tables, Trees And Their Supplemental Widgets
 
 Collections are used to display lists of items, for example in tables or trees.
-The HTML elements are generated by the collection views in the [backend](devel/backend/view)
+The HTML elements are generated by the collection views in the [backend](/epigraf/devel/backend/view)
 and are supplemented by JavaScript widgets.
 
 ### TableWidget
@@ -215,7 +215,7 @@ Both are descendants of the `BaseForm` class supporting features for saving data
 - Handle form validation and the form submission lifecycle.
 - Emit events for other widgets reacting to content updates.
 
-![Inheritance hierarchy](devel/assets/img/classes-widget-basedocumentmodel.png)
+![Inheritance hierarchy](/epigraf/devel/assets/img/classes-widget-basedocumentmodel.png)
 
 The `EntityWidget` is used for simple entities, usually displayed in a vertical table.
 It inherits all methods and properties from `BaseForm`
@@ -232,7 +232,7 @@ Parts of a document may be distributed on the page. Two cases are distinguished
   The main document and the satellites both derive from `BaseDocumentPart`
   that provides some basic common methods on the frontend view layer.
 - **Subordinate** data contained within the main document widget or its satellite widgets
-  comprise, for example, sections and items (see the [model layer in the backend](devel/backend/model)).
+  comprise, for example, sections and items (see the [model layer in the backend](/epigraf/devel/backend/model)).
   Both data types have model classes and a corresponding widget class that directly derive
   from `BaseDocument` which mainly allows accessing their parent documents, table names and ID attributes.
 

docs/devel/index.md

@@ -7,11 +7,11 @@
 #
 # To modify the layout, see https://jekyllrb.com/docs/themes/#overriding-theme-defaults
 title: Welcome Developers!
-permalink: 'devel/'
+permalink: '/epigraf/devel/'
 ---
 
 *Note: You are currently reading the developer documentation.
-For information about how to use and configure Epigraf, see the [user documentation](user/).*
+For information about how to use and configure Epigraf, see the [user documentation](/epigraf/user/).*
 
 Epigraf has a history.
 You will find archeological layers and legacy code from former development epochs
@@ -23,7 +23,7 @@ Look out for the flowers that are in bloom and help nurture the garden.
 ## Getting Started
 
 Epigraf is a classical web application.
-The [server infrastructure](devel/servers) to run Epigraf consists of an Apache web server,
+The [server infrastructure](/epigraf/devel/servers) to run Epigraf consists of an Apache web server,
 a MariaDB database server, file storage, and optionally a Redis cache server.
 You can use the prepared docker compose setup to run the application:
 
@@ -58,18 +58,18 @@ You can use the prepared docker compose setup to run the application:
    with the username `admin` and the password `admin`.
 
 What's next?
-Before you proceed, get familiar with the [core concepts](user/coreconcepts/) of Epigraf.
-Then learn how to [adapt Epigraf](user/configuration/) to your use case.
+Before you proceed, get familiar with the [core concepts](/epigraf/user/coreconcepts/) of Epigraf.
+Then learn how to [adapt Epigraf](/epigraf/user/configuration/) to your use case.
 
 ## Architecture
 
-The [frontend](devel/frontend) is rendered in the browser using HTML, CSS, and JavaScript. Frontend logic is based on the EpiWidJs framework.
-The [backend](devel/backend) is implemented using the CakePHP framework and contains the application logic.
-MariaDB and the file system is used to store [data](devel/database). There is one application database for managing
+The [frontend](/epigraf/devel/frontend) is rendered in the browser using HTML, CSS, and JavaScript. Frontend logic is based on the EpiWidJs framework.
+The [backend](/epigraf/devel/backend) is implemented using the CakePHP framework and contains the application logic.
+MariaDB and the file system is used to store [data](/epigraf/devel/database). There is one application database for managing
 user accounts and application-wide data. For the research data, multiple project databases are created.
 Frontend and database content is cached using Redis. If no Redis server is available, the cache is stored in the file system.
 
-![Epigraf architecture](devel/assets/img/epigraf-architecture.png)
+![Epigraf architecture](/epigraf/devel/assets/img/epigraf-architecture.png)
 
 ## Directory structure
 

docs/devel/tast/index.md

@@ -6,13 +6,13 @@ toc: false
 
 Throughout the development process, Epigraf code is tested in three ways:
 
-- [Backend tests](devel/tests/backend) use PHPUnit. They call endpoints and test whether the output
+- [Backend tests](/epigraf/devel/tests/backend) use PHPUnit. They call endpoints and test whether the output
   matches the expectations. This tests model, view, and controllers of the backend at the same.
   Unit tests are performed by the same method as integration tests,
   but check the functionality of specific model and utility classes.
   Unit tests compare function outputs (and database content modified by functions) with the expected results.
-- [Frontend tests](devel/tests/frontend) use Jest and check JavaScript code from the widgets.
-- [Acceptance tests](devel/tests/acceptance) use Codeception. They check the appearance and interactivity of the frontend
+- [Frontend tests](/epigraf/devel/tests/frontend) use Jest and check JavaScript code from the widgets.
+- [Acceptance tests](/epigraf/devel/tests/acceptance) use Codeception. They check the appearance and interactivity of the frontend
   by performing actions in a real browser. This includes testing the backend code since
   the frontend is generated by the backend.
 

docs/user/administration/databases.md

@@ -1,6 +1,6 @@
 ---
 title: Database Administration
-permalink: 'user/administration/databases/'
+permalink: '/epigraf/user/administration/databases/'
 ---
 
 Epigraf manages separate databases for different projects.