diff --git a/Dockerfile b/Dockerfile
index ce53096cda9ed1f9e47249960cd603cf39077398..2e68793b73f116399b6bbad4feb45faadc37485b 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -30,8 +30,10 @@ RUN \
 
 # Import self-signed cert as trusted CA
 RUN \
-  openssl s_client -servername cert.codemate.se -connect codemate.se:443 </dev/null | sed -ne '/--BEGIN CERTIFICATE--/,/--END CERTIFICATE--/p' > /tmp/codemate.cert && \
-  keytool -import -noprompt -trustcacerts -keystore /usr/lib/jvm/java-7-oracle/jre/lib/security/cacerts -storepass changeit -noprompt -alias codemate-self-signed -file /tmp/codemate.cert
+  mkdir -p /usr/share/ca-certificates/extra && \
+  openssl s_client -servername cert.codemate.se -connect codemate.se:443 </dev/null | sed -ne '/--BEGIN CERTIFICATE--/,/--END CERTIFICATE--/p' > /usr/share/ca-certificates/extra/codemate.crt && \
+  update-ca-certificates && \
+  keytool -import -noprompt -trustcacerts -keystore /usr/lib/jvm/java-7-oracle/jre/lib/security/cacerts -storepass changeit -noprompt -alias codemate-self-signed -file /usr/share/ca-certificates/extra/codemate.crt
 
 # Install and configure Exim
 RUN \
diff --git a/README.md b/README.md
index c434427c6f6ec4b4c0c30ab7a8cd546e4aef3739..c81b89ff7eb6b653c8e3607c41334c835caacbe0 100644
--- a/README.md
+++ b/README.md
@@ -47,13 +47,20 @@ docker run -e JIRA_VERSION=6.3.1 -d registry.codemate.se/jira
 
 ### Overriding JIRA files
 
-By providing an environment variable name `JIRA_OVERLAY` that points to a gzipped tar file you can apply an overlay on the JIRA installation. This tarball will be unzipped and extracted in the root of the JIRA installation directory. The overlay enables you to add custom jira configurations such as SSL or Crowd integration.
+By providing an environment variable name `JIRA_OVERLAY` that points to a directory or URL of a gzipped tar file you can apply an overlay on the JIRA installation. A directory will be recursively copied, and a tarball will be unzipped and extracted in the root of the Confluence installation directory. The overlay enables you to add custom JIRA configurations such as SSL or Crowd integration.
 
 ```
 docker run -e JIRA_OVERLAY=http://10.0.0.1/jira-config.tgz -d registry.codemate.se/jira
+docker run -e JIRA_OVERLAY=/tmp/jira-config -d registry.codemate.se/jira
 ```
 
-The overlay is fetched using curl so if you need to provide basic auth credentials simply prefix the url with the credentials, for example:
+The overlay is fetched using curl so file URLs are valid:
+
+```
+JIRA_OVERLAY="file:///tmp/jira-config.tgz"
+```
+
+If you need to provide basic auth credentials simply prefix the url with the credentials, for example:
 
 ```
 JIRA_OVERLAY="-u username:password http://10.0.0.1/jira-config.tgz"
@@ -67,7 +74,7 @@ By providing an environment variable name `MYSQL_INIT` that points to an SQL scr
 docker run -e MYSQL_INIT=http://10.0.0.1/jira-init.sql -d registry.codemate.se/jira
 ```
 
-Basic auth credentials can be used as mentioned in the JIRA overlay section.
+Basic auth credentials and file URLs can be used as mentioned in the overlay section.
 
 ### Combined options
 
@@ -81,7 +88,6 @@ docker run \
   -e JIRA_OVERLAY=http://10.0.0.1/jira-config.tgz \
   -v /opt/application-data/jira:/home/jira \
   -p 8080:8080 \
-  -p 8081:8081 \
   -d registry.codemate.se/jira
 ```
 
diff --git a/init.sh b/init.sh
index c592a997b52d57ba24b14c10b503e4696cdd857a..8f628dff03015edd588cabc441682a178c620b8c 100644
--- a/init.sh
+++ b/init.sh
@@ -2,19 +2,19 @@
 
 set -e # Exit on errors
 
-SEPARATOR="-------------------------------------------------------------------------------"
 JIRA_DIR=/opt/atlassian-jira-$JIRA_VERSION-standalone
 MYSQL_DIR=$JIRA_HOME/mysql-data
 
 if [ ! -d $JIRA_DIR ]; then
     curl -s -v -L http://www.atlassian.com/software/jira/downloads/binary/atlassian-jira-$JIRA_VERSION.tar.gz | tar xzf - -C /opt
-    curl -s -v -L -o $JIRA_DIR/lib/mysql-connector-java-5.1.31.jar http://repo1.maven.org/maven2/mysql/mysql-connector-java/5.1.31/mysql-connector-java-5.1.31.jar
-    echo "$SEPARATOR"
 fi
 
 if [ ${JIRA_OVERLAY:+x} ] && [ -d $JIRA_DIR ]; then
-    curl -s -v -L $JIRA_OVERLAY | tar xzf - -C $JIRA_DIR
-    echo "$SEPARATOR"
+    if [ -d $JIRA_OVERLAY ]; then
+        cp -R $JIRA_OVERLAY/* $JIRA_DIR
+    else
+        curl -s -v -L $JIRA_OVERLAY | tar xzf - -C $JIRA_DIR
+    fi
 fi
 
 chown -R root:root $JIRA_DIR
@@ -30,7 +30,6 @@ if [ ! -d $MYSQL_DIR ]; then
     mysql_install_db
     mysqld_safe &
     sleep 5s
-    echo "$SEPARATOR"
 else
     mysqld_safe &
     sleep 5s
@@ -38,11 +37,9 @@ fi
 
 if [ ${MYSQL_INIT:+x} ] && [ -d $MYSQL_DIR ]; then
     curl -s -v -L $MYSQL_INIT | mysql
-    echo "$SEPARATOR"
 fi
 
 env | sort
-echo "$SEPARATOR"
 
 exim4 -v -bdf -q15m &