From 458e35c0d8ee86e1be0904d23d8fbc129c6367c2 Mon Sep 17 00:00:00 2001
From: Michael Kirsten <kirsten@kit.edu>
Date: Wed, 30 Aug 2023 04:02:17 +0200
Subject: [PATCH 1/3] Minor refactorings

---
 .../formal/virage/core/ConfigReader.java      | 73 +++++++++++--------
 .../core/VirageCommandLineInterface.java      |  2 +-
 .../isabelle/IsabelleFrameworkExtractor.java  |  6 +-
 .../virage/isabelle/ScalaIsabelleFacade.java  |  6 +-
 4 files changed, 50 insertions(+), 37 deletions(-)

diff --git a/virage/src/main/java/edu/kit/kastel/formal/virage/core/ConfigReader.java b/virage/src/main/java/edu/kit/kastel/formal/virage/core/ConfigReader.java
index 6a3532b..12f6522 100644
--- a/virage/src/main/java/edu/kit/kastel/formal/virage/core/ConfigReader.java
+++ b/virage/src/main/java/edu/kit/kastel/formal/virage/core/ConfigReader.java
@@ -121,7 +121,7 @@ public final class ConfigReader {
     /**
      * SWI-Prolog option to dump runtime variables.
      */
-    private static final String DUMP_RUNTIME_VARIABLES = " --dump-runtime-variables";
+    private static final String DUMP_RUNTIME_VARIABLES = "--dump-runtime-variables";
 
     /**
      * THe xdg-open command. Maybe only makes real sense for unix systems, but well.
@@ -220,6 +220,23 @@ public static ConfigReader getInstance() {
         return instance;
     }
 
+    /**
+     * Short-hand method for the command output within the command line interface.
+     *
+     * @param command the given command
+     * @param option the option given as parameter for the command
+     * @return the printed command output
+     * @throws IOException exception in case the process yields I/O problems
+     * @throws InterruptedException exception in case the process is interrupted
+     */
+    private static String getCommandOutput(final String command, final String option)
+            throws IOException, InterruptedException {
+        final String none = "<NONE>" + '\n';
+        final String proc = command + " " + option;
+        final String output = ProcessUtils.runTerminatingProcess(proc).getFirstValue();
+        return output.isEmpty() ? none : output;
+    }
+
     /**
      * Checks whether all external software is available and prints the version numbers of said
      * software.
@@ -233,12 +250,9 @@ public String checkAvailabilityAndGetVersions() {
 
         // ISABELLE
         try {
-            res += "Isabelle: \t\t"
-                    + ProcessUtils.runTerminatingProcess(this.getIsabelleExecutable() + " version")
-                    .getFirstValue();
-            res += "Scala (via Isabelle): " + ProcessUtils
-                    .runTerminatingProcess(this.getIsabelleExecutable() + " scalac -version")
-            .getFirstValue();
+            final String isaExec = this.getIsabelleExecutable();
+            res += "Isabelle: \t\t" + getCommandOutput(isaExec, "version");
+            res += "Scala (via Isabelle): " + getCommandOutput(isaExec + " scalac", "-version");
         } catch (final IOException e) {
             res += "Isabelle: \t\tNOT FOUND\n";
             this.isabelleAvailable = false;
@@ -250,9 +264,8 @@ public String checkAvailabilityAndGetVersions() {
 
         // SWIPL
         try {
-            res += "SWI-Prolog: \t\t" + ProcessUtils
-                    .runTerminatingProcess(this.properties.get(SWIPL_BIN) + " --version")
-            .getFirstValue();
+            res += "SWI-Prolog: \t\t"
+                    + getCommandOutput((String)this.properties.get(SWIPL_BIN), "--version");
         } catch (final IOException e) {
             System.out.println("SWI-Prolog: NOT FOUND\n");
             this.swiplAvailable = false;
@@ -306,18 +319,16 @@ private Pair<Boolean, List<String>> checkConfigCompatibility() throws IOExceptio
 
     private String computeIsabelleHome()
             throws IOException, InterruptedException, ExternalSoftwareUnavailableException {
-        final String output = ProcessUtils
-                .runTerminatingProcess(this.getIsabelleExecutable() + " getenv ISABELLE_HOME")
-                .getFirstValue();
+        final String output =
+                getCommandOutput(this.getIsabelleExecutable(), "getenv ISABELLE_HOME");
 
         return output.split(KEY_VALUE_SEPARATOR)[1].trim();
     }
 
     private String computeIsabelleSessionDir()
             throws IOException, InterruptedException, ExternalSoftwareUnavailableException {
-        final String output = ProcessUtils
-                .runTerminatingProcess(this.getIsabelleExecutable() + " getenv ISABELLE_HOME_USER")
-                .getFirstValue();
+        final String output =
+                getCommandOutput(this.getIsabelleExecutable(), "getenv ISABELLE_HOME_USER");
 
         return output.split(KEY_VALUE_SEPARATOR)[1].trim();
     }
@@ -375,7 +386,7 @@ public List<String> getAdditionalProperties() {
         String prop = this.properties.getProperty(SESSION_SPECIFIC_ASSUMPTIONS);
         prop = this.replaceTypeAliases(prop);
 
-        return this.readAndSplitList(prop);
+        return readAndSplitList(prop);
     }
 
     /**
@@ -400,7 +411,7 @@ public List<String> getAtomicTypes() {
         String prop = this.properties.getProperty("SESSION_SPECIFIC_ATOMIC_TYPES");
         prop = this.replaceTypeAliases(prop);
 
-        return this.readAndSplitList(prop);
+        return readAndSplitList(prop);
     }
 
     /**
@@ -490,7 +501,7 @@ public String getIsabelleSessionDir() throws ExternalSoftwareUnavailableExceptio
     }
 
     public List<String> getIsabelleTactics() {
-        return this.readAndSplitList(this.properties.getProperty("ISABELLE_TACTICS"));
+        return readAndSplitList(this.properties.getProperty("ISABELLE_TACTICS"));
     }
 
     public String getPathToRootFile() {
@@ -503,8 +514,8 @@ public String getPathToRootFile() {
      */
     public Map<String, String> getComponentAliases() {
         final Map<String, String> toReturn = new HashMap<String, String>();
-        final List<String> pairStrings = this.readAndSplitList(
-                this.properties.getProperty(COMPONENT_ALIASES));
+        final List<String> pairStrings =
+                readAndSplitList(this.properties.getProperty(COMPONENT_ALIASES));
 
         for(final String pairString: pairStrings) {
             final String[] elements = pairString.split(PAIR_SEPARATOR);
@@ -527,9 +538,9 @@ public String getSwiplHome() throws ExternalSoftwareUnavailableException {
 
         if (this.swiplHome == null) {
             try {
-                final String output = ProcessUtils.runTerminatingProcess(
-                        this.properties.getProperty(SWIPL_BIN) + DUMP_RUNTIME_VARIABLES)
-                        .getFirstValue();
+                final String output =
+                        getCommandOutput(this.properties.getProperty(SWIPL_BIN),
+                                         DUMP_RUNTIME_VARIABLES);
                 final String[] lines = output.split(System.lineSeparator());
                 String value = "";
                 for (final String line : lines) {
@@ -569,9 +580,9 @@ public String getSwiplLib() throws ExternalSoftwareUnavailableException {
 
         if (this.swiplLib == null) {
             try {
-                final String output = ProcessUtils.runTerminatingProcess(
-                        this.properties.getProperty(SWIPL_BIN) + DUMP_RUNTIME_VARIABLES)
-                        .getFirstValue();
+                final String output =
+                        getCommandOutput(this.properties.getProperty(SWIPL_BIN),
+                                         DUMP_RUNTIME_VARIABLES);
                 final String[] lines = output.split(System.lineSeparator());
                 String value = "";
                 String path = "";
@@ -633,7 +644,7 @@ public List<Pair<String, String>> getTypeSynonyms() throws IllegalArgumentExcept
 
         String prop = this.properties.getProperty("SESSION_SPECIFIC_TYPE_SYNONYMS");
         prop = this.replaceTypeAliases(prop);
-        final List<String> typeSynonyms = this.readAndSplitList(prop);
+        final List<String> typeSynonyms = readAndSplitList(prop);
 
         for (final String synonym : typeSynonyms) {
             final String synonymCopy = this.replaceTypeAliases(synonym);
@@ -722,7 +733,7 @@ public void openConfigFileForEditing() throws ExternalSoftwareUnavailableExcepti
         }
     }
 
-    private List<String> readAndSplitList(final String list) {
+    private static List<String> readAndSplitList(final String list) {
         final String[] splits = list.split(LIST_SEPARATOR);
 
         final List<String> result = new LinkedList<String>();
@@ -789,8 +800,8 @@ private String replaceTypeAliases(final String s) {
             return copyOfs;
         }
 
-        final List<String> replacements = this
-                .readAndSplitList(this.properties.getProperty(SESSION_SPECIFIC_TYPE_ALIASES));
+        final List<String> replacements =
+                readAndSplitList(this.properties.getProperty(SESSION_SPECIFIC_TYPE_ALIASES));
 
         final Map<String, String> replMap = new HashMap<String, String>();
 
diff --git a/virage/src/main/java/edu/kit/kastel/formal/virage/core/VirageCommandLineInterface.java b/virage/src/main/java/edu/kit/kastel/formal/virage/core/VirageCommandLineInterface.java
index 382f600..a1670fd 100644
--- a/virage/src/main/java/edu/kit/kastel/formal/virage/core/VirageCommandLineInterface.java
+++ b/virage/src/main/java/edu/kit/kastel/formal/virage/core/VirageCommandLineInterface.java
@@ -232,7 +232,7 @@ private void setupLibswipl() {
                 newValue = this.requestString(StringUtils.appendPeriod("Please input the path to "
                         + LIBSWIPL_SO) + " "
                         + "For your setup of SWI-Prolog, typical values are "
-                        + this.addQuotationsToPath("/usr/lib/" + LIBSWIPL_SO) + "or "
+                        + this.addQuotationsToPath("/usr/lib/" + LIBSWIPL_SO) + " or "
                         + this.addQuotationsToPath(
                                 ConfigReader.getInstance().getSwiplLib() + LIBSWIPL_SO)
                         + ", but"
diff --git a/virage/src/main/java/edu/kit/kastel/formal/virage/isabelle/IsabelleFrameworkExtractor.java b/virage/src/main/java/edu/kit/kastel/formal/virage/isabelle/IsabelleFrameworkExtractor.java
index 09e2e89..68abd8d 100644
--- a/virage/src/main/java/edu/kit/kastel/formal/virage/isabelle/IsabelleFrameworkExtractor.java
+++ b/virage/src/main/java/edu/kit/kastel/formal/virage/isabelle/IsabelleFrameworkExtractor.java
@@ -201,7 +201,7 @@ private String convertIsabelleToProlog(final String s) {
 
         final String copyOfs = s.strip();
 
-        for (int i = 0; i < copyOfs.length(); i++) {
+        for (int i = 0; i < copyOfs.length();) {
             final char cur = copyOfs.charAt(i);
 
             switch (cur) {
@@ -218,11 +218,11 @@ private String convertIsabelleToProlog(final String s) {
                     if (endIdx < copyOfs.length() - 1 && copyOfs.charAt(endIdx + 1) != ')') {
                         res += PrologPredicate.SEPARATOR;
                     }
-                    // Checkstyle does not like this, I think it is reasonable here.
                     i = endIdx + 1;
                 } else {
                     insideBrackets = true;
                     res += cur;
+                    i++;
                 }
                 break;
             case ' ':
@@ -232,9 +232,11 @@ private String convertIsabelleToProlog(final String s) {
                     res += '(';
                     insideBrackets = true;
                 }
+                i++;
                 break;
             default:
                 res += cur;
+                i++;
                 break;
             }
         }
diff --git a/virage/src/main/java/edu/kit/kastel/formal/virage/isabelle/ScalaIsabelleFacade.java b/virage/src/main/java/edu/kit/kastel/formal/virage/isabelle/ScalaIsabelleFacade.java
index 7c2a31b..ecd2c99 100644
--- a/virage/src/main/java/edu/kit/kastel/formal/virage/isabelle/ScalaIsabelleFacade.java
+++ b/virage/src/main/java/edu/kit/kastel/formal/virage/isabelle/ScalaIsabelleFacade.java
@@ -134,7 +134,7 @@ public ScalaIsabelleFacade(final String sessionDirValue, final String sessionNam
                     + " the session manually within Isabelle "
                     + "might help. If the session is supposed"
                     + " to generate documentation, "
-                    + "texlive is required!");
+                    + "TeX Live is required!");
             throw new IsabelleBuildFailedException();
         }
         this.init();
@@ -175,7 +175,7 @@ public static void buildSession(final String sessionDir, final String sessionNam
             LOGGER.error("Building session " + sessionName
                     + " failed. Restarting ViRAGe or building"
                     + " the session manually within Isabelle might help. If the session is supposed"
-                    + " to generate documentation, texlive is required!");
+                    + " to generate documentation, TeX Live is required!");
             throw new IsabelleBuildFailedException();
         }
 
@@ -346,7 +346,7 @@ private void init() {
     /**
      * Required, as StringConverter cannot be instantiated.
      */
-    private static class JavaStringConverter extends Converter<String> {
+    private static final class JavaStringConverter extends Converter<String> {
 
         @Override
         public String exnToValue(final Isabelle localIsabelle, final ExecutionContext ec) {

From 56494fa00b2ba1be611f10ff7af8820ec96a75bd Mon Sep 17 00:00:00 2001
From: Michael Kirsten <kirsten@kit.edu>
Date: Wed, 30 Aug 2023 04:02:33 +0200
Subject: [PATCH 2/3] More updates to pom file

---
 virage/pom.xml | 53 ++++++++++++++++++++++++++++----------------------
 1 file changed, 30 insertions(+), 23 deletions(-)

diff --git a/virage/pom.xml b/virage/pom.xml
index 426fc4c..ca52502 100644
--- a/virage/pom.xml
+++ b/virage/pom.xml
@@ -41,10 +41,10 @@
     <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
     <project.reporting.outputEncoding>UTF-8</project.reporting.outputEncoding>
     <maven.version>3.8.1</maven.version>
-    <maven.compiler.release>11</maven.compiler.release>
-    <maven.compiler.source>11</maven.compiler.source>
-    <maven.compiler.target>11</maven.compiler.target>
-    <jdk.version>11</jdk.version>
+    <maven.compiler.release>17</maven.compiler.release>
+    <maven.compiler.source>17</maven.compiler.source>
+    <maven.compiler.target>17</maven.compiler.target>
+    <jdk.version>17</jdk.version>
     <exec.mainClass>edu.kit.kastel.formal.virage.core.VirageMain</exec.mainClass>
   </properties>
 
@@ -94,7 +94,7 @@
     <dependency>
       <groupId>com.github.SWI-Prolog</groupId>
       <artifactId>packages-jpl</artifactId>
-      <version>V9.1.7</version>  <!-- version 7.6.1 of JPL -->
+      <version>V9.1.14</version>  <!-- version 7.6.1 of JPL -->
     </dependency>
     <!-- https://mvnrepository.com/artifact/commons-cli/commons-cli -->
     <dependency>
@@ -105,12 +105,12 @@
     <dependency>
       <groupId>commons-io</groupId>
       <artifactId>commons-io</artifactId>
-      <version>2.11.0</version>
+      <version>2.13.0</version>
     </dependency>
     <dependency>
       <groupId>com.fasterxml.jackson.core</groupId>
       <artifactId>jackson-databind</artifactId>
-      <version>2.14.2</version>
+      <version>2.15.2</version>
     </dependency>
     <!-- <dependency> <groupId>com.github.VeriVote</groupId> <artifactId>ViRAGe</artifactId>
       <version>master-SNAPSHOT</version> </dependency> -->
@@ -125,7 +125,7 @@
     <dependency>
       <groupId>org.apache.commons</groupId>
       <artifactId>commons-configuration2</artifactId>
-      <version>2.8.0</version>
+      <version>2.9.0</version>
     </dependency>
     <dependency>
       <groupId>commons-beanutils</groupId>
@@ -181,7 +181,7 @@
       <plugin>
         <groupId>org.apache.maven.plugins</groupId>
         <artifactId>maven-enforcer-plugin</artifactId>
-        <version>3.2.1</version>
+        <version>3.4.0</version>
         <executions>
           <execution>
             <id>enforce-versions</id>
@@ -205,14 +205,14 @@
         <version>3.2.4</version> <executions> <execution> <phase>package</phase> 
         <goals> <goal>shade</goal> </goals> <configuration> <transformers> <transformer 
         implementation="org.apache.maven.plugins.shade.resource.ManifestResourceTransformer"> 
-        <mainClass>edu.kit.kastel.formal.virage.core.VirageMain</mainClass> <manifestEntries> 
+        <mainClass>${exec.mainClass}</mainClass> <manifestEntries>
         <Multi-Release>true</Multi-Release> </manifestEntries> </transformer> <transformer 
         implementation="org.apache.maven.plugins.shade.resource.ServicesResourceTransformer" 
         /> </transformers> </configuration> </execution> </executions> </plugin> -->
       <plugin>
         <groupId>org.codehaus.mojo</groupId>
         <artifactId>versions-maven-plugin</artifactId>
-        <version>2.15.0</version>
+        <version>2.16.0</version>
         <configuration>
           <rulesUri>file:///${basedir}/rules.xml</rulesUri>
           <allowSnapshots>false</allowSnapshots>
@@ -231,9 +231,10 @@
       <plugin>
         <groupId>org.codehaus.mojo</groupId>
         <artifactId>properties-maven-plugin</artifactId>
-        <version>1.1.0</version>
+        <version>1.2.0</version>
         <executions>
           <execution>
+            <id>read-settings</id>
             <phase>process-resources</phase>
             <goals>
               <goal>read-project-properties</goal>
@@ -253,7 +254,7 @@
       <plugin>
         <groupId>org.apache.maven.plugins</groupId>
         <artifactId>maven-surefire-plugin</artifactId>
-        <version>3.0.0</version>
+        <version>3.1.2</version>
         <configuration>
           <!-- Unit tests take ages, deployment tests are obsolete as ViRAGe performs 
             these checks at runtime. -->
@@ -270,7 +271,7 @@
           </execution>
         </executions>
         <configuration>
-          <mainClass>edu.kit.kastel.formal.virage.core.VirageMain</mainClass>
+          <mainClass>${exec.mainClass}</mainClass>
           <environmentVariables>
             <LD_PRELOAD>${SWI_PROLOG_LIBSWIPL_PATH}</LD_PRELOAD>
             <LD_LIBRARY_PATH>${SWI_PROLOG_LIBRARIES_PATH}</LD_LIBRARY_PATH>
@@ -289,12 +290,12 @@
         <plugin>
           <groupId>org.apache.maven.plugins</groupId>
           <artifactId>maven-clean-plugin</artifactId>
-          <version>3.2.0</version>
+          <version>3.3.1</version>
         </plugin>
         <plugin>
           <groupId>org.apache.maven.plugins</groupId>
           <artifactId>maven-resources-plugin</artifactId>
-          <version>3.3.0</version>
+          <version>3.3.1</version>
         </plugin>
         <plugin>
           <groupId>org.apache.maven.plugins</groupId>
@@ -305,16 +306,23 @@
           <groupId>org.apache.maven.plugins</groupId>
           <artifactId>maven-jar-plugin</artifactId>
           <version>3.3.0</version>
+          <configuration>
+            <archive>
+              <manifest>
+                <mainClass>${exec.mainClass}</mainClass>
+              </manifest>
+            </archive>
+          </configuration>
         </plugin>
         <plugin>
           <groupId>org.apache.maven.plugins</groupId>
           <artifactId>maven-install-plugin</artifactId>
-          <version>3.1.0</version>
+          <version>3.1.1</version>
         </plugin>
         <plugin>
           <groupId>org.apache.maven.plugins</groupId>
           <artifactId>maven-deploy-plugin</artifactId>
-          <version>3.1.0</version>
+          <version>3.1.1</version>
         </plugin>
         <plugin>
           <groupId>org.apache.maven.plugins</groupId>
@@ -327,14 +335,13 @@
         <plugin>
           <groupId>org.apache.maven.plugins</groupId>
           <artifactId>maven-checkstyle-plugin</artifactId>
-          <version>3.2.1</version>
+          <version>3.3.0</version>
           <configuration>
             <failsOnError>false</failsOnError>
             <includeTestSourceDirectory>true</includeTestSourceDirectory>
             <includeResources>true</includeResources>
             <includeTestResources>true</includeTestResources>
             <configLocation>checks.xml</configLocation>
-            <encoding>UTF-8</encoding>
             <consoleOutput>true</consoleOutput>
             <failsOnError>true</failsOnError>
             <linkXRef>false</linkXRef>
@@ -343,14 +350,14 @@
             <dependency>
               <groupId>com.puppycrawl.tools</groupId>
               <artifactId>checkstyle</artifactId>
-              <version>10.9.2</version>
+              <version>10.12.3</version>
             </dependency>
           </dependencies>
         </plugin>
         <plugin>
           <groupId>com.github.spotbugs</groupId>
           <artifactId>spotbugs-maven-plugin</artifactId>
-          <version>4.7.3.2</version>
+          <version>4.7.3.5</version>
           <configuration>
             <xmlOutput>true</xmlOutput>
             <failOnError>false</failOnError>
@@ -378,7 +385,7 @@
       <plugin>
         <groupId>org.apache.maven.plugins</groupId>
         <artifactId>maven-project-info-reports-plugin</artifactId>
-        <version>3.4.2</version>
+        <version>3.4.5</version>
         <reportSets>
           <reportSet>
             <reports>

From 0d60d9cfa57eeb5b80f78503a42472d876daae5d Mon Sep 17 00:00:00 2001
From: Michael Kirsten <kirsten@kit.edu>
Date: Sat, 2 Sep 2023 17:24:36 +0200
Subject: [PATCH 3/3] A few small fixes, mainly regarding environment
 variables. Still need to have a look at the call to Scala-Isabelle

---
 virage/pom.xml                                | 57 +++++++----
 .../kit/kastel/formal/util/ProcessUtils.java  | 97 +++++++++++--------
 .../kit/kastel/formal/util/SystemUtils.java   |  9 +-
 .../formal/virage/core/ConfigReader.java      |  9 +-
 .../core/VirageCommandLineInterface.java      |  7 +-
 .../virage/isabelle/ScalaIsabelleFacade.java  | 36 ++++---
 virage/src/main/resources/settings            |  8 +-
 7 files changed, 131 insertions(+), 92 deletions(-)

diff --git a/virage/pom.xml b/virage/pom.xml
index ca52502..8994d5c 100644
--- a/virage/pom.xml
+++ b/virage/pom.xml
@@ -41,11 +41,17 @@
     <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
     <project.reporting.outputEncoding>UTF-8</project.reporting.outputEncoding>
     <maven.version>3.8.1</maven.version>
+    <maven.clean.version>3.3.1</maven.clean.version>
+    <maven.install.version>3.1.1</maven.install.version>
+    <maven.jar.version>3.3.0</maven.jar.version>
     <maven.compiler.release>17</maven.compiler.release>
     <maven.compiler.source>17</maven.compiler.source>
     <maven.compiler.target>17</maven.compiler.target>
     <jdk.version>17</jdk.version>
-    <exec.mainClass>edu.kit.kastel.formal.virage.core.VirageMain</exec.mainClass>
+    <log4j.version>2.20.0</log4j.version>
+    <spotbugs.version>4.7.3</spotbugs.version>
+    <swi.home.dir>/usr/lib/swi-prolog</swi.home.dir>
+    <main.class>edu.kit.kastel.formal.virage.core.VirageMain</main.class>
   </properties>
 
   <distributionManagement>
@@ -83,12 +89,17 @@
     <dependency>
       <groupId>org.apache.logging.log4j</groupId>
       <artifactId>log4j-api</artifactId>
-      <version>2.20.0</version>
+      <version>${log4j.version}</version>
     </dependency>
     <dependency>
       <groupId>org.apache.logging.log4j</groupId>
       <artifactId>log4j-core</artifactId>
-      <version>2.20.0</version>
+      <version>${log4j.version}</version>
+    </dependency>
+    <dependency>
+      <groupId>org.apache.logging.log4j</groupId>
+      <artifactId>log4j-slf4j-impl</artifactId>
+      <version>${log4j.version}</version>
     </dependency>
     <!-- JPL bidirectional Prolog-Java: https://github.com/SWI-Prolog/packages-jpl -->
     <dependency>
@@ -205,7 +216,7 @@
         <version>3.2.4</version> <executions> <execution> <phase>package</phase> 
         <goals> <goal>shade</goal> </goals> <configuration> <transformers> <transformer 
         implementation="org.apache.maven.plugins.shade.resource.ManifestResourceTransformer"> 
-        <mainClass>${exec.mainClass}</mainClass> <manifestEntries>
+        <mainClass>${main.class}</mainClass> <manifestEntries>
         <Multi-Release>true</Multi-Release> </manifestEntries> </transformer> <transformer 
         implementation="org.apache.maven.plugins.shade.resource.ServicesResourceTransformer" 
         /> </transformers> </configuration> </execution> </executions> </plugin> -->
@@ -220,6 +231,7 @@
         </configuration>
         <executions>
           <execution>
+            <id>versions-display</id>
             <phase>compile</phase>
             <goals>
               <goal>display-dependency-updates</goal>
@@ -235,7 +247,7 @@
         <executions>
           <execution>
             <id>read-settings</id>
-            <phase>process-resources</phase>
+            <phase>initialize</phase>
             <goals>
               <goal>read-project-properties</goal>
             </goals>
@@ -267,21 +279,24 @@
         <version>3.1.0</version>
         <executions>
           <execution>
-            <phase>test</phase>
+            <id>execute</id>
+            <goals>
+              <goal>exec</goal>
+            </goals>
           </execution>
         </executions>
         <configuration>
-          <mainClass>${exec.mainClass}</mainClass>
-          <environmentVariables>
-            <LD_PRELOAD>${SWI_PROLOG_LIBSWIPL_PATH}</LD_PRELOAD>
-            <LD_LIBRARY_PATH>${SWI_PROLOG_LIBRARIES_PATH}</LD_LIBRARY_PATH>
-          </environmentVariables>
           <executable>java</executable>
+          <mainClass>${main.class}</mainClass>
           <arguments>
             <argument>-classpath</argument>
             <classpath />
-            <argument>edu.kit.kastel.formal.virage.core.VirageMain</argument>
+            <argument>${main.class}</argument>
           </arguments>
+          <environmentVariables>
+            <SWI_HOME_DIR>${swi.home.dir}</SWI_HOME_DIR>
+            <LD_PRELOAD>${swi.home.dir}/lib/x86_64-linux/libswipl.so</LD_PRELOAD>
+          </environmentVariables>
         </configuration>
       </plugin>
     </plugins>
@@ -290,12 +305,12 @@
         <plugin>
           <groupId>org.apache.maven.plugins</groupId>
           <artifactId>maven-clean-plugin</artifactId>
-          <version>3.3.1</version>
+          <version>${maven.clean.version}</version>
         </plugin>
         <plugin>
           <groupId>org.apache.maven.plugins</groupId>
           <artifactId>maven-resources-plugin</artifactId>
-          <version>3.3.1</version>
+          <version>${maven.clean.version}</version>
         </plugin>
         <plugin>
           <groupId>org.apache.maven.plugins</groupId>
@@ -305,11 +320,11 @@
         <plugin>
           <groupId>org.apache.maven.plugins</groupId>
           <artifactId>maven-jar-plugin</artifactId>
-          <version>3.3.0</version>
+          <version>${maven.jar.version}</version>
           <configuration>
             <archive>
               <manifest>
-                <mainClass>${exec.mainClass}</mainClass>
+                <mainClass>${main.class}</mainClass>
               </manifest>
             </archive>
           </configuration>
@@ -317,12 +332,12 @@
         <plugin>
           <groupId>org.apache.maven.plugins</groupId>
           <artifactId>maven-install-plugin</artifactId>
-          <version>3.1.1</version>
+          <version>${maven.install.version}</version>
         </plugin>
         <plugin>
           <groupId>org.apache.maven.plugins</groupId>
           <artifactId>maven-deploy-plugin</artifactId>
-          <version>3.1.1</version>
+          <version>${maven.install.version}</version>
         </plugin>
         <plugin>
           <groupId>org.apache.maven.plugins</groupId>
@@ -335,7 +350,7 @@
         <plugin>
           <groupId>org.apache.maven.plugins</groupId>
           <artifactId>maven-checkstyle-plugin</artifactId>
-          <version>3.3.0</version>
+          <version>${maven.jar.version}</version>
           <configuration>
             <failsOnError>false</failsOnError>
             <includeTestSourceDirectory>true</includeTestSourceDirectory>
@@ -357,7 +372,7 @@
         <plugin>
           <groupId>com.github.spotbugs</groupId>
           <artifactId>spotbugs-maven-plugin</artifactId>
-          <version>4.7.3.5</version>
+          <version>${spotbugs.version}.5</version>
           <configuration>
             <xmlOutput>true</xmlOutput>
             <failOnError>false</failOnError>
@@ -373,7 +388,7 @@
             <dependency>
               <groupId>com.github.spotbugs</groupId>
               <artifactId>spotbugs</artifactId>
-              <version>4.7.3</version>
+              <version>${spotbugs.version}</version>
             </dependency>
           </dependencies>
         </plugin>
diff --git a/virage/src/main/java/edu/kit/kastel/formal/util/ProcessUtils.java b/virage/src/main/java/edu/kit/kastel/formal/util/ProcessUtils.java
index a0c29c2..602f6ae 100644
--- a/virage/src/main/java/edu/kit/kastel/formal/util/ProcessUtils.java
+++ b/virage/src/main/java/edu/kit/kastel/formal/util/ProcessUtils.java
@@ -18,16 +18,16 @@ public class ProcessUtils {
     private static final Logger LOGGER = LogManager.getLogger(ProcessUtils.class);
 
     /**
-     * Executes a terminating command and logs it outputs, stderr foing to logger.warn(), stdout to
-     * logger.info(). <b>Does not return if the command is non-terminating!</b>
+     * Executes a terminating command and prints its output to System.out/System.err, respectively.
+     * <b>Does not return if the command is non-terminating!</b>
      *
      * @param command the command to be executed (as is, i.e. the String has to contain all
      *      parameters etc.)
-     * @return the exit code (usually 0 on success, but depending on the command)
+     * @return a Pair of strings representing stdout and stderr of the process
      * @throws IOException if reading the outputs fails
      * @throws InterruptedException if command execution is interrupted
      */
-    public static int runTerminatingProcessAndLogOutput(final String command)
+    public static Output runTerminatingProcess(final String command)
             throws IOException, InterruptedException {
         final Runtime rt = Runtime.getRuntime();
 
@@ -37,19 +37,12 @@ public static int runTerminatingProcessAndLogOutput(final String command)
         final String stdErr = new String(p.getErrorStream().readAllBytes(), StandardCharsets.UTF_8);
         final String stdOut = new String(p.getInputStream().readAllBytes(), StandardCharsets.UTF_8);
 
-        if (!stdErr.isEmpty()) {
-            LOGGER.warn(stdErr);
-        }
-        if (!stdOut.isEmpty()) {
-            LOGGER.info(stdOut);
-        }
-
-        return status;
+        return new Output(stdOut, stdErr, status);
     }
 
     /**
-     * Executes a terminating command and prints its output to System.out/System.err, respectively.
-     * <b>Does not return if the command is non-terminating!</b>
+     * Executes a terminating command and logs it outputs, stderr going to logger.warn(), stdout to
+     * logger.info(). <b>Does not return if the command is non-terminating!</b>
      *
      * @param command the command to be executed (as is, i.e. the String has to contain all
      *      parameters etc.)
@@ -57,24 +50,16 @@ public static int runTerminatingProcessAndLogOutput(final String command)
      * @throws IOException if reading the outputs fails
      * @throws InterruptedException if command execution is interrupted
      */
-    public static int runTerminatingProcessAndPrintOutput(final String command)
+    public static int runTerminatingProcessAndLogOutput(final String command)
             throws IOException, InterruptedException {
-        final Runtime rt = Runtime.getRuntime();
-
-        final Process p = rt.exec(StringUtils.stripAndEscape(command));
-        final int status = p.waitFor();
-
-        final String stdErr = new String(p.getErrorStream().readAllBytes(), StandardCharsets.UTF_8);
-        final String stdOut = new String(p.getInputStream().readAllBytes(), StandardCharsets.UTF_8);
-
-        if (!stdErr.isEmpty()) {
-            System.err.print(stdErr);
+        final Output output = runTerminatingProcess(command);
+        if (!output.stdErr.isEmpty()) {
+            LOGGER.warn(output.stdErr);
         }
-        if (!stdOut.isEmpty()) {
-            System.out.print(stdOut);
+        if (!output.stdOut.isEmpty()) {
+            LOGGER.info(output.stdOut);
         }
-
-        return status;
+        return output.status;
     }
 
     /**
@@ -83,20 +68,54 @@ public static int runTerminatingProcessAndPrintOutput(final String command)
      *
      * @param command the command to be executed (as is, i.e. the String has to contain all
      *      parameters etc.)
-     * @return a Pair of strings representing stdout and stderr of the process
+     * @return the exit code (usually 0 on success, but depending on the command)
      * @throws IOException if reading the outputs fails
      * @throws InterruptedException if command execution is interrupted
      */
-    public static Pair<String, String> runTerminatingProcess(final String command)
+    public static int runTerminatingProcessAndPrintOutput(final String command)
             throws IOException, InterruptedException {
-        final Runtime rt = Runtime.getRuntime();
-
-        final Process p = rt.exec(StringUtils.stripAndEscape(command));
-        p.waitFor();
-
-        final String stdErr = new String(p.getErrorStream().readAllBytes(), StandardCharsets.UTF_8);
-        final String stdOut = new String(p.getInputStream().readAllBytes(), StandardCharsets.UTF_8);
+        final Output output = runTerminatingProcess(command);
+        if (!output.stdErr.isEmpty()) {
+            System.err.print(output.stdErr);
+        }
+        if (!output.stdOut.isEmpty()) {
+            System.out.print(output.stdOut);
+        }
+        return output.status;
+    }
 
-        return new Pair<String, String>(stdOut, stdErr);
+    /**
+     * The static data structure to store the text from the standard output and the error output
+     * stream as well as the integer status value.
+     *
+     * @author VeriVote
+     */
+    public static class Output {
+        /**
+         * The standard output stream as a string.
+         */
+        public final String stdOut;
+        /**
+         * The error output stream as a string.
+         */
+        public final String stdErr;
+        /**
+         * The status output as an integer value.
+         */
+        public final int status;
+
+        /**
+         * Constructor method for the static data structure to store the text from the standard
+         * output and the error output stream as well as the integer status value.
+         *
+         * @param outStream The standard output stream as a string.
+         * @param errStream The error output stream as a string.
+         * @param statusValue The status output as an integer value.
+         */
+        public Output(final String outStream, final String errStream, final int statusValue) {
+            stdOut = outStream;
+            stdErr = errStream;
+            status = statusValue;
+        }
     }
 }
diff --git a/virage/src/main/java/edu/kit/kastel/formal/util/SystemUtils.java b/virage/src/main/java/edu/kit/kastel/formal/util/SystemUtils.java
index 6ee726d..64607c7 100644
--- a/virage/src/main/java/edu/kit/kastel/formal/util/SystemUtils.java
+++ b/virage/src/main/java/edu/kit/kastel/formal/util/SystemUtils.java
@@ -7,7 +7,7 @@
 import java.lang.reflect.Field;
 import java.nio.charset.StandardCharsets;
 import java.nio.file.Files;
-import java.time.LocalDateTime;
+import java.time.ZonedDateTime;
 import java.time.format.DateTimeFormatter;
 import java.util.Map;
 
@@ -67,13 +67,12 @@ public static void addDirToLibraryPath(final String s) throws IOException {
     }
 
     /**
-     * Returns current time (yyyy-MM-dd HH:mm:ss).
+     * Returns current time (yyyy-MM-dd HH:mm:ss OOOO).
      * @return the time
      */
     public static String getTime() {
-        final DateTimeFormatter dtf = DateTimeFormatter.ofPattern("yyyy-MM-dd HH:mm:ss");
-        final LocalDateTime now = LocalDateTime.now();
-
+        final DateTimeFormatter dtf = DateTimeFormatter.ofPattern("yyyy-MM-dd HH:mm:ss OOOO");
+        final ZonedDateTime now = ZonedDateTime.now();
         return dtf.format(now);
     }
 
diff --git a/virage/src/main/java/edu/kit/kastel/formal/virage/core/ConfigReader.java b/virage/src/main/java/edu/kit/kastel/formal/virage/core/ConfigReader.java
index 12f6522..4b4753a 100644
--- a/virage/src/main/java/edu/kit/kastel/formal/virage/core/ConfigReader.java
+++ b/virage/src/main/java/edu/kit/kastel/formal/virage/core/ConfigReader.java
@@ -233,8 +233,9 @@ private static String getCommandOutput(final String command, final String option
             throws IOException, InterruptedException {
         final String none = "<NONE>" + '\n';
         final String proc = command + " " + option;
-        final String output = ProcessUtils.runTerminatingProcess(proc).getFirstValue();
-        return output.isEmpty() ? none : output;
+        final ProcessUtils.Output output = ProcessUtils.runTerminatingProcess(proc);
+        final String result = output.stdOut.isEmpty() ? output.stdErr : output.stdOut;
+        return result.isEmpty() ? none : result;
     }
 
     /**
@@ -758,7 +759,9 @@ public void readConfigFile(final boolean overwriteIfNecessary) throws IOExceptio
         final File virageDir = new File(virageFolderPath);
         this.configFile = new File(configPath);
         if (!this.configFile.exists()) {
-            Files.createDirectory(virageDir.toPath());
+            if (!virageDir.exists()) {
+                Files.createDirectory(virageDir.toPath());
+            }
             Files.createFile(this.configFile.toPath());
             this.copyConfigToExpectedPath();
         }
diff --git a/virage/src/main/java/edu/kit/kastel/formal/virage/core/VirageCommandLineInterface.java b/virage/src/main/java/edu/kit/kastel/formal/virage/core/VirageCommandLineInterface.java
index a1670fd..4d422b2 100644
--- a/virage/src/main/java/edu/kit/kastel/formal/virage/core/VirageCommandLineInterface.java
+++ b/virage/src/main/java/edu/kit/kastel/formal/virage/core/VirageCommandLineInterface.java
@@ -8,8 +8,6 @@
 import java.io.StringWriter;
 import java.io.Writer;
 import java.nio.charset.StandardCharsets;
-import java.time.LocalDateTime;
-import java.time.format.DateTimeFormatter;
 import java.util.ArrayList;
 import java.util.Collections;
 import java.util.LinkedList;
@@ -699,10 +697,9 @@ private void printSettings() {
     }
 
     private void printTimestamp() {
-        final DateTimeFormatter dtf = DateTimeFormatter.ofPattern("yyyy-MM-dd HH:mm:ss");
-        final LocalDateTime now = LocalDateTime.now();
+        final String now = SystemUtils.getTime();
         this.displayMessage(HEADER_LINE_START + "Version " + VirageCore.getVersion()
-                + ", Timestamp: " + dtf.format(now));
+                + ", Timestamp: " + now);
         this.displayMessage(HEADER_LINE_START + "If you need help, type \"help\", \"h\" or \"?\".");
         this.displayMessage(HEADER_LINE_START + "To exit ViRAGe, type \"exit\".");
     }
diff --git a/virage/src/main/java/edu/kit/kastel/formal/virage/isabelle/ScalaIsabelleFacade.java b/virage/src/main/java/edu/kit/kastel/formal/virage/isabelle/ScalaIsabelleFacade.java
index ecd2c99..f4aecff 100644
--- a/virage/src/main/java/edu/kit/kastel/formal/virage/isabelle/ScalaIsabelleFacade.java
+++ b/virage/src/main/java/edu/kit/kastel/formal/virage/isabelle/ScalaIsabelleFacade.java
@@ -112,14 +112,18 @@ public ScalaIsabelleFacade(final String sessionDirValue, final String sessionNam
 
         final List<Path> sessionDirs = new LinkedList<Path>();
         sessionDirs.add(Path.of(this.sessionDir));
-
-        this.setup = new Setup(Path.of(ConfigReader.getInstance().getIsabelleHome()),
-                sessionNameValue,
-                new Some<Path>(Path.of(ConfigReader.getInstance().getIsabelleSessionDir())),
-                Path.of(sessionDirValue),
-                JavaConverters.asScalaIteratorConverter(sessionDirs.iterator()).asScala().toSeq(),
-                true, true /*try verbose first*/, null, null /* try to get away with null first */);
-
+        final String isabelleHome = ConfigReader.getInstance().getIsabelleHome();
+        this.setup = // JIsabelle.setupSetBuild(true, JIsabelle.setup(Path.of(isabelleHome)));
+                new Setup(Path.of(isabelleHome),
+                          sessionNameValue,
+                          new Some<Path>(
+                                  Path.of(ConfigReader.getInstance().getIsabelleSessionDir())),
+                          Path.of(sessionDirValue),
+                          JavaConverters.asScalaIteratorConverter(
+                                  sessionDirs.iterator()).asScala().toSeq(),
+                          true, true /*try verbose first*/,
+                          (Isabelle i) -> i.exceptionManager(),
+                          null /* try to get away with null first */);
         try {
             isabelle = new Isabelle(this.setup);
             // Scala has no checked Exceptions and the constructor is not annotated.
@@ -158,13 +162,15 @@ public static void buildSession(final String sessionDir, final String sessionNam
         final List<Path> sessionDirs = new LinkedList<Path>();
         sessionDirs.add(Path.of(new File(sessionDir).getAbsolutePath()));
 
-        final Setup setup = new Setup(Path.of(ConfigReader.getInstance().getIsabelleHome()),
-                sessionName,
-                new Some<Path>(Path.of(ConfigReader.getInstance().getIsabelleSessionDir())),
-                Path.of(sessionDir),
-                JavaConverters.asScalaIteratorConverter(sessionDirs.iterator()).asScala().toSeq(),
-                true, true /*try verbose first*/, null, null /* try to get away with null first */);
-
+        final Setup setup =
+                new Setup(Path.of(ConfigReader.getInstance().getIsabelleHome()),
+                        sessionName,
+                        new Some<Path>(Path.of(ConfigReader.getInstance().getIsabelleSessionDir())),
+                        Path.of(sessionDir),
+                        JavaConverters.asScalaIteratorConverter(sessionDirs.iterator())
+                            .asScala().toSeq(),
+                        true, true /*try verbose first*/, (Isabelle i) -> i.exceptionManager(),
+                        null /* try to get away with null first */);
         try {
             isabelle = new Isabelle(setup);
             isabelle.destroy();
diff --git a/virage/src/main/resources/settings b/virage/src/main/resources/settings
index cf031f5..ba54cb3 100644
--- a/virage/src/main/resources/settings
+++ b/virage/src/main/resources/settings
@@ -1,4 +1,4 @@
-TIMESTAMP=
+TIMESTAMP=2023-09-01 00:00:00 GMT+02:00
 
 # This value is used for internal consistency checks, please do not alter it!
 VIRAGE_CONFIG_VERSION=0.1.0
@@ -13,11 +13,11 @@ GCC_EXECUTABLE=gcc
 SWI_PROLOG_EXECUTABLE=swipl
 
 # Path to libswipl.so
-SWI_PROLOG_LIBSWIPL_PATH=
+SWI_PROLOG_LIBSWIPL_PATH=/usr/lib/swi-prolog/lib/x86_64-linux/libswipl.so
 
 # Path to the SWI-Prolog library (usually, $SWI_HOME_DIR/lib/$ARCHITECTURE
 # should contain libjpl.so, otherwise install swi-prolog-java)
-SWI_PROLOG_LIBRARIES_PATH=
+SWI_PROLOG_LIBRARIES_PATH=/usr/lib/swi-prolog/lib/x86_64-linux/
 
 
 ## System settings
@@ -28,7 +28,7 @@ SYSTEM_DEFAULT_OUTPUT_PATH=./target/generated-sources/
 
 # Custom text editor (only used when xdg-open fails; if empty, environment
 # variable $EDITOR is used).
-SYSTEM_TEXT_EDITOR=
+SYSTEM_TEXT_EDITOR=/usr/bin/kate
 
 
 ## Isabelle settings