diff --git a/.classpath b/.classpath
index 31348801353..cad91ee2b18 100644
--- a/.classpath
+++ b/.classpath
@@ -8,8 +8,8 @@
 	<classpathentry kind="src" path="base/common/src/test/java"/>
 	<classpathentry excluding="**/CMakeLists.txt" kind="src" path="base/common/examples/java"/>
 	<classpathentry kind="src" path="base/tools/src/main/java"/>
-	<classpathentry excluding="**/CMakeLists.txt" kind="src" path="base/server/tomcat/src"/>
-	<classpathentry excluding="**/CMakeLists.txt" kind="src" path="base/server/tomcat-9.0/src"/>
+	<classpathentry kind="src" path="base/tomcat/src/main/java"/>
+	<classpathentry kind="src" path="base/tomcat-9.0/src/main/java"/>
 	<classpathentry kind="src" path="base/server/src/main/java"/>
 	<classpathentry kind="src" path="base/server/src/test/java"/>
 	<classpathentry kind="src" path="base/ca/src/main/java"/>
diff --git a/base/CMakeLists.txt b/base/CMakeLists.txt
index cb03ed0bf47..fed8335e99d 100644
--- a/base/CMakeLists.txt
+++ b/base/CMakeLists.txt
@@ -394,6 +394,7 @@ if (BUILD_PKI_CORE OR BUILD_PKI_CONSOLE)
 
     if(WITH_SERVER)
 
+        add_subdirectory(${APP_SERVER})
         add_subdirectory(server)
 
         list(APPEND PKI_JAVADOC_SOURCEPATH
diff --git a/base/server/CMakeLists.txt b/base/server/CMakeLists.txt
index 86c855baa0d..891f6d70004 100644
--- a/base/server/CMakeLists.txt
+++ b/base/server/CMakeLists.txt
@@ -1,7 +1,5 @@
 project(server)
 
-add_subdirectory(${APP_SERVER})
-add_subdirectory(tomcat)
 add_subdirectory(cmsbundle)
 add_subdirectory(healthcheck)
 
diff --git a/base/server/tomcat-9.0/CMakeLists.txt b/base/server/tomcat-9.0/CMakeLists.txt
deleted file mode 100644
index a6f7a52a05f..00000000000
--- a/base/server/tomcat-9.0/CMakeLists.txt
+++ /dev/null
@@ -1,10 +0,0 @@
-project(server-tomcat-8.5)
-
-add_subdirectory(src)
-
-install(
-    DIRECTORY
-        conf/
-    DESTINATION
-        ${DATA_INSTALL_DIR}/server/conf/
-)
diff --git a/base/server/tomcat/CMakeLists.txt b/base/server/tomcat/CMakeLists.txt
deleted file mode 100644
index 8c862145ec5..00000000000
--- a/base/server/tomcat/CMakeLists.txt
+++ /dev/null
@@ -1,3 +0,0 @@
-project(server-tomcat)
-
-add_subdirectory(src)
diff --git a/base/server/tomcat/src/CMakeLists.txt b/base/server/tomcat/src/CMakeLists.txt
deleted file mode 100644
index 1c31a9f0fac..00000000000
--- a/base/server/tomcat/src/CMakeLists.txt
+++ /dev/null
@@ -1 +0,0 @@
-project(pki-tomcat)
diff --git a/base/server/tomcat-9.0/src/CMakeLists.txt b/base/tomcat-9.0/CMakeLists.txt
similarity index 65%
rename from base/server/tomcat-9.0/src/CMakeLists.txt
rename to base/tomcat-9.0/CMakeLists.txt
index 7871db6678b..78d43e168a2 100644
--- a/base/server/tomcat-9.0/src/CMakeLists.txt
+++ b/base/tomcat-9.0/CMakeLists.txt
@@ -1,10 +1,10 @@
-project(pki-tomcat-8.5)
+project(pki-tomcat-9.0)
 
 # build pki-tomcat
 javac(pki-tomcat-classes
     SOURCES
-        ../../tomcat/src/*.java
-        *.java
+        ../tomcat/src/main/java/*.java
+        src/main/java/*.java
     CLASSPATH
         ${SERVLET_JAR}
         ${JAXRS_API_JAR}
@@ -15,25 +15,27 @@ javac(pki-tomcat-classes
         ${JSS_JAR} ${TOMCATJSS_JAR}
         ${PKI_CMSUTIL_JAR}
     OUTPUT_DIR
-        ${CMAKE_BINARY_DIR}/../../tomcat
+        ${CMAKE_BINARY_DIR}/../tomcat
     DEPENDS
         pki-cmsutil-jar pki-tools-jar
 )
 
 configure_file(
-    ${CMAKE_CURRENT_SOURCE_DIR}/pki-tomcat.mf
-    ${CMAKE_CURRENT_BINARY_DIR}/pki-tomcat.mf
+    ${CMAKE_CURRENT_SOURCE_DIR}/src/main/resources/META-INF/MANIFEST.MF
+    ${CMAKE_CURRENT_BINARY_DIR}/MANIFEST.MF
 )
 
+set(PKI_TOMCAT_JAR ${CMAKE_BINARY_DIR}/dist/pki-tomcat.jar CACHE INTERNAL "pki-tomcat jar file")
+
 jar(pki-tomcat-jar
     CREATE
         ${CMAKE_BINARY_DIR}/dist/pki-tomcat.jar
     OPTIONS
         m
     PARAMS
-        ${CMAKE_CURRENT_BINARY_DIR}/pki-tomcat.mf
+        ${CMAKE_CURRENT_BINARY_DIR}/MANIFEST.MF
     INPUT_DIR
-        ${CMAKE_BINARY_DIR}/../../tomcat
+        ${CMAKE_BINARY_DIR}/../tomcat
     DEPENDS
         pki-tomcat-classes
 )
@@ -45,4 +47,9 @@ install(
         ${JAVA_JAR_INSTALL_DIR}/pki
 )
 
-set(PKI_TOMCAT_JAR ${CMAKE_BINARY_DIR}/dist/pki-tomcat.jar CACHE INTERNAL "pki-tomcat jar file")
+install(
+    DIRECTORY
+        conf/
+    DESTINATION
+        ${DATA_INSTALL_DIR}/server/conf/
+)
diff --git a/base/server/tomcat-9.0/conf/Catalina/localhost/ROOT.xml b/base/tomcat-9.0/conf/Catalina/localhost/ROOT.xml
similarity index 100%
rename from base/server/tomcat-9.0/conf/Catalina/localhost/ROOT.xml
rename to base/tomcat-9.0/conf/Catalina/localhost/ROOT.xml
diff --git a/base/server/tomcat-9.0/conf/Catalina/localhost/pki.xml b/base/tomcat-9.0/conf/Catalina/localhost/pki.xml
similarity index 100%
rename from base/server/tomcat-9.0/conf/Catalina/localhost/pki.xml
rename to base/tomcat-9.0/conf/Catalina/localhost/pki.xml
diff --git a/base/server/tomcat-9.0/conf/catalina.properties b/base/tomcat-9.0/conf/catalina.properties
similarity index 100%
rename from base/server/tomcat-9.0/conf/catalina.properties
rename to base/tomcat-9.0/conf/catalina.properties
diff --git a/base/server/tomcat-9.0/conf/server.xml b/base/tomcat-9.0/conf/server.xml
similarity index 100%
rename from base/server/tomcat-9.0/conf/server.xml
rename to base/tomcat-9.0/conf/server.xml
diff --git a/base/server/tomcat-9.0/src/com/netscape/cms/tomcat/ProxyRealm.java b/base/tomcat-9.0/src/main/java/com/netscape/cms/tomcat/ProxyRealm.java
similarity index 100%
rename from base/server/tomcat-9.0/src/com/netscape/cms/tomcat/ProxyRealm.java
rename to base/tomcat-9.0/src/main/java/com/netscape/cms/tomcat/ProxyRealm.java
diff --git a/base/server/tomcat-9.0/src/com/netscape/cms/tomcat/SSLAuthenticatorWithFallback.java b/base/tomcat-9.0/src/main/java/com/netscape/cms/tomcat/SSLAuthenticatorWithFallback.java
similarity index 100%
rename from base/server/tomcat-9.0/src/com/netscape/cms/tomcat/SSLAuthenticatorWithFallback.java
rename to base/tomcat-9.0/src/main/java/com/netscape/cms/tomcat/SSLAuthenticatorWithFallback.java
diff --git a/base/server/tomcat-9.0/src/pki-tomcat.mf b/base/tomcat-9.0/src/main/resources/META-INF/MANIFEST.MF
similarity index 100%
rename from base/server/tomcat-9.0/src/pki-tomcat.mf
rename to base/tomcat-9.0/src/main/resources/META-INF/MANIFEST.MF
diff --git a/base/server/tomcat/src/com/netscape/cms/tomcat/AbstractPKIAuthenticator.java b/base/tomcat/src/main/java/com/netscape/cms/tomcat/AbstractPKIAuthenticator.java
similarity index 100%
rename from base/server/tomcat/src/com/netscape/cms/tomcat/AbstractPKIAuthenticator.java
rename to base/tomcat/src/main/java/com/netscape/cms/tomcat/AbstractPKIAuthenticator.java
diff --git a/base/server/tomcat/src/com/netscape/cms/tomcat/ExternalAuthenticationValve.java b/base/tomcat/src/main/java/com/netscape/cms/tomcat/ExternalAuthenticationValve.java
similarity index 100%
rename from base/server/tomcat/src/com/netscape/cms/tomcat/ExternalAuthenticationValve.java
rename to base/tomcat/src/main/java/com/netscape/cms/tomcat/ExternalAuthenticationValve.java
diff --git a/base/server/tomcat/src/com/netscape/cms/tomcat/ExternalPrincipal.java b/base/tomcat/src/main/java/com/netscape/cms/tomcat/ExternalPrincipal.java
similarity index 100%
rename from base/server/tomcat/src/com/netscape/cms/tomcat/ExternalPrincipal.java
rename to base/tomcat/src/main/java/com/netscape/cms/tomcat/ExternalPrincipal.java
diff --git a/base/server/tomcat/src/com/netscape/cms/tomcat/NuxwdogPasswordStore.java b/base/tomcat/src/main/java/com/netscape/cms/tomcat/NuxwdogPasswordStore.java
similarity index 100%
rename from base/server/tomcat/src/com/netscape/cms/tomcat/NuxwdogPasswordStore.java
rename to base/tomcat/src/main/java/com/netscape/cms/tomcat/NuxwdogPasswordStore.java
diff --git a/base/server/tomcat/src/com/netscape/cms/tomcat/PKIListener.java b/base/tomcat/src/main/java/com/netscape/cms/tomcat/PKIListener.java
similarity index 100%
rename from base/server/tomcat/src/com/netscape/cms/tomcat/PKIListener.java
rename to base/tomcat/src/main/java/com/netscape/cms/tomcat/PKIListener.java
diff --git a/base/server/tomcat/src/org/dogtagpki/tomcat/PKITrustManager.java b/base/tomcat/src/main/java/org/dogtagpki/tomcat/PKITrustManager.java
similarity index 100%
rename from base/server/tomcat/src/org/dogtagpki/tomcat/PKITrustManager.java
rename to base/tomcat/src/main/java/org/dogtagpki/tomcat/PKITrustManager.java