DOC: merge README_CONFIGURATION.md and configuration.rst

TODO

• @sina fix reference to README_CONFIGURATION.md in README_SETUP.md: reference should point to doc/administration/configuration.rst

src/doc/administration/configuration.rst

-Configuration
-=============
+Server Configuration
+====================
 
-The server is configured through configuration files. There are two directories with config files:
+Main Configuration File
+-----------------------
 
-``conf/core``
-   Upstream defaults are stored here.
-``conf/ext``
-   User specific configuration should be stored here, settings in ``ext`` override settings in
-   ``core``.  Additionally, configuration files may be stored in ``*.d`` directories here, named
-   after the original config file name.  For example, the general server configuration will be
-   assembled from ``conf/core/server.conf``, ``conf/ext/server.conf`` and any ``*.conf`` files found
-   in ``conf/ext/server.conf.d``.
+The server is configured through configuration files. The main file is the
+`server.conf`.
 
-Configuration files
--------------------
+The `server.conf` is a list of key-value pairs. A configuration file may
+contain empty lines, comment lines, and key-value lines.  Comment lines begin
+with a hash (`#`). Key-value lines must have the format `KEY_NAME=VALUE` or
+`KEY_NAME = VALUE`.
 
-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.indiscale.com/caosdb/src/caosdb-server/-/blob/dev/conf/core/server.conf>`__.
+The server default configuration is located at `./conf/core/server.conf`.
+Upstream defaults are stored here. The possible configuration options are
+documented inside the
+`default file <https://gitlab.indiscale.com/caosdb/src/caosdb-server/-/blob/dev/conf/core/server.conf>`__.
+
+User specific configuration should be in `./conf/ext/` and  override settings
+in `./conf/core/`.
+
+The default configuration can be overriden by
+
+    1. the file ./conf/ext/server.conf
+
+    2. any file in ./conf/ext/server.conf.d/ in (approximately?) alphabetical order
+
+    3. environment variables with the prefix `CAOSDB_CONFIG_`
+
+in this order.
+
+Further Configuration Files
+---------------------------
+
+Further settings are to be set in files which are by default stored in `./conf/core/`:
 
 ``global_entity_permissions.xml``
-   :doc:`Permissions<../Permissions>` which are automatically set, based on user roles.  See the
+   :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>`__.
 
@@ -39,8 +53,10 @@ In each of these directories, the server looks for the following files:
 
 ``authtoken.yaml``
    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
+   without the need of a user/password combination. One-time Authentication Tokens can be configure
+   to be issued for special purposes (e.g. a call of a server-side script or initial setup after the server start)
+   or to be written to a file on a regular basis. An example of a configuration is located at `./conf/core/authtoken.example.yaml`.
+   There is more documentation inside the `template file
    <https://gitlab.indiscale.com/caosdb/src/caosdb-server/-/blob/dev/conf/core/authtoken.example.yaml>`__.
 
 ``cache.ccf``
@@ -54,6 +70,9 @@ In each of these directories, the server looks for the following files:
    <https://logging.apache.org/log4j/2.x/>`_.  The ``default`` file is always loaded, in debug mode
    the ``debug`` file iss added as well.
 
+The administrator may set the corresponding options in the main configuration
+file (`./conf/core/server.conf` and it's friends) to replace these special
+files with custom configuration.
 
 Changing the configuration at runtime
 -------------------------------------