[fix] Copy configuration files then modify them

See https://github.com/YunoHost-Apps/dokuwiki_ynh/pull/37#issuecomment-398374816

"Since a few time, because the conf folder will be kept for later uses (especially in change_url), it's better to copy your file in the right place before modifying it."

scripts/install

@@ -100,15 +100,6 @@ ynh_add_fpm_config
 # CUSTOMIZE DOKUWIKI
 #=================================================
 
-# Set the "admin" user
-ynh_replace_string "__YNH_ADMIN_USER__" "$admin"  "../conf/local.protected.php"
-
-# Set the "language"
-ynh_replace_string "__YNH_LANGUAGE__" "$language" "../conf/local.php"
-
-
-# Copy Yunohost specific configuration
-
 # Loading order of configuration files
 #
 # By default DokuWiki loads its configuration files in the following order:
@@ -119,13 +110,23 @@ ynh_replace_string "__YNH_LANGUAGE__" "$language" "../conf/local.php"
 #
 # See https://www.dokuwiki.org/plugin:config#protecting_settings
 
-cp ../conf/local.protected.php $final_path/conf
+
+### Copy Yunohost specific configuration
 # This File cannot be modified directly by Dokuwiki, only by hand or by Yunohost
 # It will only be updated by Yunohost package or directly by adventurous users
+cp ../conf/local.protected.php $final_path/conf
+
+# Set the "admin" user
+ynh_replace_string "__YNH_ADMIN_USER__" "$admin"    "$final_path/conf/local.protected.php"
+
 
-cp ../conf/local.php           $final_path/conf
 # This file might be modified by dokuwiki admin panel or by plugins
 # It will not be modified by Yunohost in order to keep user settings
+cp ../conf/local.php           $final_path/conf
+
+# Set the "language"
+ynh_replace_string "__YNH_LANGUAGE__"   "$language" "$final_path/conf/local.php"
+
 
 # Restrict user rights by enforcing "read-only" mode for all users
 # See https://www.dokuwiki.org/acl#background_info
@@ -144,11 +145,11 @@ cp ../conf/acl.auth.php $final_path/conf
 cp $final_path/conf/local.php.dist      $final_path/conf/local.php.bak
 cp $final_path/conf/users.auth.php.dist $final_path/conf/users.auth.php
 
-cp $final_path/inc/preload.php.dist     $final_path/inc/preload.php
 # This file might be used by plugins like https://www.dokuwiki.org/plugin:siteexport
 # Create it to be more "user friendly" as over the top security is not the main goal here
 # This file could be use for bad behaviour.
 # See https://www.dokuwiki.org/devel:preload?s[]=preload
+cp $final_path/inc/preload.php.dist     $final_path/inc/preload.php
 
 # There is no template .dist provided inside DokuWiki installation folder
 # Create "empty" files to be able to manage linux permissions
@@ -158,11 +159,10 @@ cp ../conf/plugins.local.php            $final_path/conf/plugins.local.php.bak
 
 # Create file if it does not exist
 if [ ! -f "$final_path/conf/local.protected.php" ]; then
-	# Set the default "admin"
-	# Replace string in order to have a functionnal configuration file
-	ynh_replace_string "__YNH_ADMIN_USER__" "$admin" "../conf/local.protected.php"
-
 	cp ../conf/local.protected.php $final_path/conf
+
+	# Set the default "admin"
+	ynh_replace_string "__YNH_ADMIN_USER__" "$admin" "$final_path/conf/local.protected.php"
 fi
 
 #=================================================

scripts/upgrade

@@ -56,6 +56,7 @@ if [ -z "$language" ]; then
 fi
 
 
+
 # Yunohost specific configuration, if not exists
 
 # Previously, these settings were store a unique "dokuwiki.php"
@@ -75,22 +76,20 @@ fi
 # Configuration dedicated to Yunohost (LDAP and admin mainly)
 # Create file if it does not exist
 if [ ! -f "$final_path/conf/local.protected.php" ]; then
-	# Set the default "admin"
-	# Replace string in order to have a functionnal configuration file
-	ynh_replace_string "__YNH_ADMIN_USER__" "$admin" "../conf/local.protected.php"
-
 	cp ../conf/local.protected.php $final_path/conf
+
+	# Set the default "admin"
+	ynh_replace_string "__YNH_ADMIN_USER__" "$admin" "$final_path/conf/local.protected.php"
 fi
 
 # Do not overwrite existing dokuwiki configuration as it could have user customization's and settings.
 # Cannot use helper "ynh_backup_if_checksum_is_different"
 # Create file if it does not exist
 if [ ! -f "$final_path/conf/local.php" ]; then
-	# Set the default "language" only when file does not exist beforehand
-	# Replace string in order to have a functionnal configuration file
-	ynh_replace_string "__YNH_LANGUAGE__" "$language" "../conf/local.php"
-
 	cp ../conf/local.php $final_path/conf
+
+	# Set the default "language"
+	ynh_replace_string "__YNH_LANGUAGE__" "$language" "$final_path/conf/local.php"
 fi
 
 # Do not overwrite existing ACL configuration file as it could have user customization's and settings.
@@ -240,13 +239,13 @@ done
 # Safe here as this file is only used by Yunohost. Dokuwiki cannot modified it.
 ynh_backup_if_checksum_is_different "$final_path/conf/local.protected.php"
 
-# Set the "admin" user
-ynh_replace_string "__YNH_ADMIN_USER__" "$admin"  "../conf/local.protected.php"
-
 cp ../conf/local.protected.php $final_path/conf
 # This File cannot be modified directly by Dokuwiki, only by hand or by Yunohost
 # It will only be updated by Yunohost package or directly by adventurous users
 
+# Set the "admin" user
+ynh_replace_string "__YNH_ADMIN_USER__" "$admin"  "../conf/local.protected.php"
+
 # Recalculate and store the config file checksum into the app settings
 ynh_store_file_checksum "$final_path/conf/local.protected.php"