DOC: Mention the caosdb-proto submodule.

README_SETUP.md

@@ -58,12 +58,14 @@ libpam0g-dev`. Then try again.
 After a fresh clone of the repository, this is what you need to setup the
 server:
 
-1. Compile the server with `make compile`. This may take a while and there
+1. Install the `proto` submodule (and submodules for those extensions you want, see above):
+   `git submodule update --init caosdb-proto`
+2. Compile the server with `make compile`. This may take a while and there
    needs to be an internet connection as packages are downloaded to be
    integrated in the java file.
    1. It is recommended to run the unit tests with `make test`. It may take a
       while.
-2. Create an SSL certificate somewhere with a `Java Key Store` file.  For
+3. Create an SSL certificate somewhere with a `Java Key Store` file.  For
    self-signed certificates (not recommended for production use) you can do:
    - `mkdir certificates; cd certificates`
    - `keytool -genkey -keyalg RSA -alias selfsigned -keystore caosdb.jks -validity 375 -keysize 2048 -ext san=dns:localhost`
@@ -77,11 +79,11 @@ server:
    Alternatively, you can create a keystore from certificate files that you already have:
    - `openssl pkcs12 -export -inkey privkey.pem -in fullchain.pem -out all-certs.pkcs12`
    - `keytool -importkeystore -srckeystore all-certs.pkcs12 -srcstoretype PKCS12  -deststoretype pkcs12 -destkeystore caosdb.jks`
-3. Install/configure the MySQL back-end: see the `README_SETUP.md` of the
+4. Install/configure the MySQL back-end: see the `README_SETUP.md` of the
    `caosdb-mysqlbackend` repository
-4. Create an authtoken config (e.g. copy `conf/core/authtoken.example.yaml` to
+5. Create an authtoken config (e.g. copy `conf/core/authtoken.example.yaml` to
    `conf/ext/authtoken.yml` and change it)
-5. Copy `conf/core/server.conf` to `conf/ext/server.conf` and change it
+6. Copy `conf/core/server.conf` to `conf/ext/server.conf` and change it
    appropriately:
     * Setup for MySQL back-end:
       specify the fields `MYSQL_USER_NAME`, `MYSQL_USER_PASSWORD`,
@@ -94,7 +96,7 @@ server:
       `CERTIFICATES_KEY_STORE_PATH`, and `CERTIFICATES_KEY_STORE_PASSWORD`.
       Make sure that the conf file is not readable by other users because the
       certificate passwords are stored in plaintext.
-    - Set the path to the authtoken config (see step 4)
+    * Set the path to the authtoken config (see step 4)
     * Set the file system paths:
       - `FILE_SYSTEM_ROOT`: The root for all the files managed by CaosDB.
       - `DROP_OFF_BOX`: Files can be put here for insertion into CaosDB.
@@ -112,8 +114,8 @@ server:
       - `INSERT_FILES_IN_DIR_ALLOWED_DIRS`: add mounted filesystems here that
         shall be accessible by CaosDB
     * Maybe set another `SESSION_TIMEOUT_MS`.
-    * See also [CONFIGURATION.rst](src/doc/administration/configuration.rst)
-6. Copy `conf/core/usersources.ini.template` to `conf/ext/usersources.ini`.
+     * See also [CONFIGURATION.rst](src/doc/administration/configuration.rst)
+7. Copy `conf/core/usersources.ini.template` to `conf/ext/usersources.ini`.
     * You can skip this if you do not want to use an external authentication. 
       Local users (CaosDB realm) are always available.
     * Define the users/groups who you want to include/exclude.
@@ -128,7 +130,7 @@ server:
       Especially that there are no `properties` (aka `keys`) without a
       `value`. An emtpy value can be represented by `""`. Comments are
       everything from `#` or `;` to the end of the line.
-7. Possibly install the PAM caller in `misc/pam_authentication/` if you have 
+8. Possibly install the PAM caller in `misc/pam_authentication/` if you have
    not do so already. See above.
    
 Done!