Document server code structure

Document the server code structure: Schedules, Jobs, Transactions, BackendTransactions and backend specific implementations.

---

Summary

This MR introduces documentation for the server's code structure.

Additionally, a lot of documentation files received smaller fixes, for example dead links were replaced.

Focus

• Is the documentation content correct?
• Can the documentation be understood by new developers?
• Are the documentation pages (html and images) produced correctly?

Test Environment

• make doc, then direct your browser to build/doc/html/development/structure.html
• Test artefact generates by the pipeline (deploy > pages_prepare).

Check List for the Author

Please, prepare your MR for a review. Be sure to write a summary and a focus and create gitlab comments for the reviewer. They should guide the reviewer through the changes, explain your changes and also point out open questions. For further good practices have a look at our review guidelines

• All automated tests pass
• Reference related Issues
• Up-to-date CHANGELOG.md
• Annotations in code (Gitlab comments)
  • Intent of new code
  • Problems with old code
  • Why this implementation?

Check List for the Reviewer

• I understand the intent of this MR
• All automated tests pass
• Up-to-date CHANGELOG.md
• The test environment setup works and the intended behaviour is reproducible in the test environment
• In-code documentation and comments are up-to-date.
• Check: Are there specifications? Are they satisfied?
• Removed f-doc-structure line from .gitlab-ci.yml before merging.

For further good practices have a look at our review guidelines.

src/doc/administration/configuration.rst

@@ -19,18 +19,21 @@ In each of these directories, the server looks for the following files:
 
 ``server.conf``
    General server configuration options.  The possible configuration options are documented inside
-   the `default file <https://gitlab.com/caosdb/caosdb-server/-/blob/dev/conf/core/server.conf>`_.
+   the `default file
+   <https://gitlab.indiscale.com/caosdb/src/caosdb-server/-/blob/dev/conf/core/server.conf>`__.
 
 ``global_entity_permissions.xml``
-   :ref:`Permissions <concepts:Permissions>` which are automatically set, based on user roles.
-   See the `default file <https://gitlab.com/caosdb/caosdb-server/-/blob/dev/conf/core/global_entity_permissions.xml>`_.
+   :doc:`Permissions<../Permissions>` which are automatically set, based on user roles.  See the
+   `default file
+   <https://gitlab.indiscale.com/caosdb/src/caosdb-server/-/blob/dev/conf/core/global_entity_permissions.xml>`__.
 
 ``usersources.ini``
    This file defines possible sources which are checked when a user tries to authenticate.  Each
    defined source has a special section, the possible options are defined separately for each user
    source.  At the moment the best place to look for this specific documentation is at the API
    documentation of :java:type:`UserSource` and its implementing classes.  The provided `template
-   file <https://gitlab.com/caosdb/caosdb-server/-/blob/dev/conf/core/usersources.ini.template>`_
+   file
+   <https://gitlab.indiscale.com/caosdb/src/caosdb-server/-/blob/dev/conf/core/usersources.ini.template>`__
    also has some information.  The general concept about authentication realms is described in
    :java:type:`UserSources`.
 
@@ -38,13 +41,13 @@ In each of these directories, the server looks for the following files:
    Configuration for dispensed authentication tokens, which can be used to authenticate to CaosDB
    without the need of a user/password combination.  Possible use cases are server-side scripts or
    initial setup after the server start.  There is more documentation inside the `template file
-   <https://gitlab.com/caosdb/caosdb-server/-/blob/dev/conf/core/authtoken.example.yaml>`_.
+   <https://gitlab.indiscale.com/caosdb/src/caosdb-server/-/blob/dev/conf/core/authtoken.example.yaml>`__.
 
 ``cache.ccf``
    Configuration for the Java Caching System (JCS) which can be used by the server.  More
    documentation is `upstream
    <http://commons.apache.org/proper/commons-jcs/getting_started/intro.html>`_ and inside `the file
-   <https://gitlab.com/caosdb/caosdb-server/-/blob/dev/conf/core/cache.ccf>`_.
+   <https://gitlab.indiscale.com/caosdb/src/caosdb-server/-/blob/dev/conf/core/cache.ccf>`_.
 
 ``log4j2-default.properties``, ``log4j2-debug.properties``
    Configuration for logging, following the standard described by the `log4j library