diff --git a/run.sh b/run.sh
index ddd77072dd0a6afe866f2791f5e264aa47d11bbd..4b1d32851ffb3af409870b92befc86a02efda9eb 100644
--- a/run.sh
+++ b/run.sh
@@ -1 +1 @@
-mvn exec:java -Dexec.mainClass="fr.emse.gitlab.saref.Main" -Dexec.args="-d ../saref-core"
+mvn exec:java -Dexec.args="-d ../saref-core"
diff --git a/src/main/java/fr/emse/gitlab/saref/Constants.java b/src/main/java/fr/emse/gitlab/saref/Constants.java
index 1946b65e336b7bc2a3e05b1e2b97de9a78a67f01..b76665f0fe73603aa0a944343d267d6840fe80ee 100644
--- a/src/main/java/fr/emse/gitlab/saref/Constants.java
+++ b/src/main/java/fr/emse/gitlab/saref/Constants.java
@@ -34,7 +34,6 @@ public class Constants {
 	public static final String STATIC_TARGET_DIR = SITE_DIR + File.separator + "static";
 
 	public static final String SAREF_ACCESS_TOKEN = "SAREF_ACCESS_TOKEN";
-
 	public static final String SAREF_ACCESS_USERNAME = "SAREF_ACCESS_USERNAME";
 	
 	public static final String propertyFile = ".saref-repositories";
diff --git a/src/main/java/fr/emse/gitlab/saref/Main.java b/src/main/java/fr/emse/gitlab/saref/Main.java
index c5f09e4ed7ae2705657554787e815c47b543e041..8102c68759e8a6c60a938585a03d856fdca82622 100644
--- a/src/main/java/fr/emse/gitlab/saref/Main.java
+++ b/src/main/java/fr/emse/gitlab/saref/Main.java
@@ -45,6 +45,7 @@ import fr.emse.gitlab.saref.jobs.WriteRDFFiles;
 import fr.emse.gitlab.saref.jobs.CheckOWLProfile;
 import fr.emse.gitlab.saref.jobs.CheckRepositoryStructure;
 import fr.emse.gitlab.saref.jobs.CheckShapes;
+import fr.emse.gitlab.saref.jobs.CopyStaticFiles;
 
 public class Main {
 
@@ -93,12 +94,13 @@ public class Main {
 		LOG.info("Starting pipeline");
 
 		doJob(new CheckRepositoryStructure(directory));
-		doJob(new CheckShapes(directory));
-		Repositories repositories = doJob(new ReadRepositories(directory));
-		Dataset dataset = doJob(new CreateDataset(directory, repositories));
-		doJob(new CopyStaticFiles(directory));
-		Set<OWLOntologyIRIMapper> mappers = doJob(new WriteRDFFiles(directory, dataset));
-		doJob(new CheckOWLProfile(directory, mappers));
+//		doJob(new CheckShapes(directory));
+//		Repositories repositories = doJob(new ReadRepositories(directory));
+//		Repositories repositories = new Repositories();
+//		Dataset dataset = doJob(new CreateDataset(directory, repositories));
+//		doJob(new CopyStaticFiles(directory));
+//		Set<OWLOntologyIRIMapper> mappers = doJob(new WriteRDFFiles(directory, dataset));
+//		doJob(new CheckOWLProfile(directory, mappers));
 		reportAndExit(0);
 	}
 
diff --git a/src/main/java/fr/emse/gitlab/saref/jobs/CheckRepositoryStructure.java b/src/main/java/fr/emse/gitlab/saref/jobs/CheckRepositoryStructure.java
index c1f89776489ebf527aec433c249f1a18771fc43e..3fe17e736c55a3bfe5ace1d01edfc35f4e219fbb 100644
--- a/src/main/java/fr/emse/gitlab/saref/jobs/CheckRepositoryStructure.java
+++ b/src/main/java/fr/emse/gitlab/saref/jobs/CheckRepositoryStructure.java
@@ -49,9 +49,7 @@ public class CheckRepositoryStructure extends AbstractJobRunner<Void> {
 	private void checkThereExistsDirectory(String dirName) {
 		final File dir = new File(directory, dirName);
 		try {
-			if (dir.isDirectory()) {
-				success(String.format("There exists a folder named `%s`", dirName));
-			} else {
+			if (!dir.isDirectory()) {
 				failure(String.format("There should exist a folder named `%s`", dirName));
 			}
 		} catch (SecurityException ex) {
diff --git a/src/main/java/fr/emse/gitlab/saref/jobs/CheckShapes.java b/src/main/java/fr/emse/gitlab/saref/jobs/CheckShapes.java
index ae8cde80bd2e48d56003a60c9d334869a2ea509a..71e8dfb16552f63f7351494c21ddfd0beeeca635 100644
--- a/src/main/java/fr/emse/gitlab/saref/jobs/CheckShapes.java
+++ b/src/main/java/fr/emse/gitlab/saref/jobs/CheckShapes.java
@@ -30,7 +30,8 @@ public class CheckShapes extends AbstractJobRunner<Void> {
 
 	static final String SELECT_VIOLATION = "PREFIX sh: <http://www.w3.org/ns/shacl#>\n"
 			+ "SELECT ?focusNode ?resultMessage ?resultPath ?value ?severity\n" + "WHERE {   \n"
-			+ "    ?violation sh:focusNode ?focusNode .\n" + "    ?violation sh:resultMessage ?resultMessage .\n"
+			+ "    ?violation sh:focusNode ?focusNode .\n"
+			+ "    ?violation sh:resultMessage ?resultMessage .\n"
 			+ "    ?violation sh:resultSeverity ?severity .\n"
 			+ "      OPTIONAL { ?violation sh:resultPath ?resultPath . }\n"
 			+ "      OPTIONAL { ?violation sh:value ?value . } \n" + "}";
diff --git a/src/main/java/fr/emse/gitlab/saref/CopyStaticFiles.java b/src/main/java/fr/emse/gitlab/saref/jobs/CopyStaticFiles.java
similarity index 82%
rename from src/main/java/fr/emse/gitlab/saref/CopyStaticFiles.java
rename to src/main/java/fr/emse/gitlab/saref/jobs/CopyStaticFiles.java
index 1bb81ab21c14954904eed379c1cb17c26b4499d8..791a939ef825e38906ff9fd383c640cee881fe5e 100644
--- a/src/main/java/fr/emse/gitlab/saref/CopyStaticFiles.java
+++ b/src/main/java/fr/emse/gitlab/saref/jobs/CopyStaticFiles.java
@@ -1,10 +1,11 @@
-package fr.emse.gitlab.saref;
+package fr.emse.gitlab.saref.jobs;
 
 import java.io.File;
 
 import org.apache.commons.io.FileUtils;
 
-import fr.emse.gitlab.saref.jobs.AbstractJobRunner;
+import fr.emse.gitlab.saref.Constants;
+import fr.emse.gitlab.saref.Main;
 
 public class CopyStaticFiles extends AbstractJobRunner<Void> {
 	
diff --git a/src/main/java/fr/emse/gitlab/saref/jobs/ReadRepositories.java b/src/main/java/fr/emse/gitlab/saref/jobs/ReadRepositories.java
index b19839917e281562f033517592cb5bcdd21b14b3..2ebe3fe5081ebea1ce123c6a1f4ca43826715664 100644
--- a/src/main/java/fr/emse/gitlab/saref/jobs/ReadRepositories.java
+++ b/src/main/java/fr/emse/gitlab/saref/jobs/ReadRepositories.java
@@ -82,6 +82,9 @@ public class ReadRepositories extends AbstractJobRunner<Repositories> {
 		File repoDir = new File(directory, Constants.GIT_DIR);
 		try {
 			FileUtils.forceDelete(repoDir);
+		} catch (IOException ex) {
+		}
+		try {
 			FileUtils.forceMkdir(repoDir);
 		} catch (IOException ex) {
 			error(String.format("Error while creating repository directory %s", repoDir.getPath()), ex);
@@ -124,7 +127,7 @@ public class ReadRepositories extends AbstractJobRunner<Repositories> {
 		} else {
 			if (console != null) {
 				username = console
-						.readLine(String.format("Please enter your EOL account username for %s:\n", hostName));
+						.readLine(String.format("Please enter your account username for %s:\n", hostName));
 			} else if (System.getenv("GITLAB_CI") != null) {
 				LOG.info("using username 'gitlab-ci-token'");
 				username = "gitlab-ci-token";
@@ -138,7 +141,7 @@ public class ReadRepositories extends AbstractJobRunner<Repositories> {
 		} else {
 			if (console != null) {
 				password = console
-						.readPassword(String.format("Please enter your EOL account password for %s:\n", hostName));
+						.readPassword(String.format("Please enter your account password for %s:\n", hostName));
 			} else if (System.getenv("GITLAB_CI") != null) {
 				password = System.getenv("CI_JOB_TOKEN").toCharArray();
 			} else {