diff --git a/.github/workflows/benchmark.yml b/.github/workflows/benchmark.yml
index 96afdcee2f..cfba250b76 100644
--- a/.github/workflows/benchmark.yml
+++ b/.github/workflows/benchmark.yml
@@ -26,7 +26,7 @@ jobs:
 
       # Build the project and publish to Maven local
       - name: Publish to Maven local
-        run: ./gradlew publishToMavenLocal -x test -x javadoc -Pversion=${{ env.releaseVersion }}
+        run: ./gradlew publishToMavenLocal -x test -x javadoc -PbuildVersion=${{ env.releaseVersion }}
 
       # Clone the DiffBenchmark repository and run benchmarks
       - name: Clone DiffBenchmark repository and run benchmarks
diff --git a/Dockerfile b/Dockerfile
index e25db1f63f..96d7961da0 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -7,9 +7,13 @@ ENV TZ=GMT
 
 COPY . /opt/refactoringminer/
 
-RUN /opt/refactoringminer/gradlew -x test -p /opt/refactoringminer build 2>/dev/null
-RUN unzip /opt/refactoringminer/build/distributions/*.zip -d /opt/refactoringminer/build/distributions
-RUN ln -s /opt/refactoringminer/build/distributions/RefactoringMiner-*/bin/RefactoringMiner /usr/bin/refactoringminer
+RUN /opt/refactoringminer/gradlew -x test -p /opt/refactoringminer build -PbuildVersion=DockerBuild 2>/dev/null
+RUN unzip /opt/refactoringminer/build/distributions/RefactoringMiner-DockerBuild.zip -d /opt/refactoringminer/build/distributions
+RUN ln -s /opt/refactoringminer/build/distributions/RefactoringMiner-DockerBuild/bin/RefactoringMiner /usr/bin/refactoringminer
 ENV LANG C.UTF-8
 EXPOSE 6789
+
+RUN mkdir -p /diff/left /diff/right
+WORKDIR /diff
+
 #ENTRYPOINT ["refactoringminer"]
diff --git a/build.gradle b/build.gradle
index 9539b941f6..bd46141b9b 100644
--- a/build.gradle
+++ b/build.gradle
@@ -9,8 +9,8 @@ plugins {
 }
 
 group = "com.github.tsantalis"
-def version = project.hasProperty('version') ?
-        project.version
+version = project.hasProperty('buildVersion') ?
+        project.buildVersion
         : '3.0.4'
 
 applicationName = rootProject.name
@@ -39,8 +39,8 @@ test {
     useJUnitPlatform()
     maxParallelForks = Runtime.runtime.availableProcessors().intdiv(2) ?: 1
     if (project.hasProperty('notoken')) {
-        exclude '**/GHRepositoryWrapperTest.java'
-        exclude '**/TestCommandLine.class'
+        exclude '**/GHRepositoryWrapperTest.*'
+        exclude '**/TestCommandLine.*'
         print 'Skipping tests that require a GitHub token'
     }
 }
@@ -55,7 +55,7 @@ dependencies {
     implementation 'io.github.java-diff-utils:java-diff-utils:4.12'
 	implementation 'com.github.gumtreediff:core:3.0.0'
 	implementation 'com.github.gumtreediff:gen.jdt:3.0.0'
-    implementation "org.jcommander:jcommander:1.83"
+    implementation 'org.jcommander:jcommander:1.83'
     testImplementation 'junit:junit:4.13.2'
     testImplementation 'org.junit.jupiter:junit-jupiter-api:5.10.0'
     testImplementation 'org.junit.jupiter:junit-jupiter-params:5.10.0'
diff --git a/src/main/java/gui/webdiff/WebDiffRunner.java b/src/main/java/gui/webdiff/WebDiffRunner.java
index 9d283f923a..8bc2f0fa23 100644
--- a/src/main/java/gui/webdiff/WebDiffRunner.java
+++ b/src/main/java/gui/webdiff/WebDiffRunner.java
@@ -69,8 +69,8 @@ public ProjectASTDiff getProjectASTDIFF(WebDiffRunner runner) throws Exception {
                         URLHelper.getPullRequestID(runner.url),
                         timeout);
                 case DIR -> new GitHistoryRefactoringMinerImpl().diffAtDirectories(
-                        runner.src,
-                        runner.dst);
+                        runner.src.toAbsolutePath().normalize(),
+                        runner.dst.toAbsolutePath().normalize());
                 case CLONED -> new GitHistoryRefactoringMinerImpl().diffAtCommit(
                         runner.repo,
                         runner.commit,