diff --git a/csharp/ql/campaigns/Solorigate/publish.sh b/csharp/ql/campaigns/Solorigate/publish.sh
index 2d1dcfa3bfb1..0c57fd6c4880 100755
--- a/csharp/ql/campaigns/Solorigate/publish.sh
+++ b/csharp/ql/campaigns/Solorigate/publish.sh
@@ -1,7 +1,7 @@
 #!/bin/sh
 set -e
 
-SOLORIGATE_ROOT="$(dirname $0)"
+SOLORIGATE_ROOT="$(readlink -f "$(dirname $0)")"
 WORKSPACE_ROOT="$SOLORIGATE_ROOT/../../../.."
 GRPS="solorigate,-test"
 
diff --git a/java/ql/automodel/publish.sh b/java/ql/automodel/publish.sh
index 04b0d3f6ac11..202cdd690a75 100755
--- a/java/ql/automodel/publish.sh
+++ b/java/ql/automodel/publish.sh
@@ -1,7 +1,7 @@
 #!/bin/sh
 set -e
 
-AUTOMODEL_ROOT="$(dirname $0)"
+AUTOMODEL_ROOT="$(readlink -f "$(dirname $0)")"
 WORKSPACE_ROOT="$AUTOMODEL_ROOT/../../../.."
 GRPS="automodel,-test"
 
diff --git a/java/ql/automodel/test/AutomodelApplicationModeExtraction/AutomodelApplicationModeExtractCandidates.qlref b/java/ql/automodel/test/AutomodelApplicationModeExtraction/AutomodelApplicationModeExtractCandidates.qlref
index b97c87be55fd..5ea712b0239a 100644
--- a/java/ql/automodel/test/AutomodelApplicationModeExtraction/AutomodelApplicationModeExtractCandidates.qlref
+++ b/java/ql/automodel/test/AutomodelApplicationModeExtraction/AutomodelApplicationModeExtractCandidates.qlref
@@ -1 +1 @@
-Telemetry/AutomodelApplicationModeExtractCandidates.ql
+AutomodelApplicationModeExtractCandidates.ql
diff --git a/java/ql/automodel/test/AutomodelApplicationModeExtraction/AutomodelApplicationModeExtractNegativeExamples.qlref b/java/ql/automodel/test/AutomodelApplicationModeExtraction/AutomodelApplicationModeExtractNegativeExamples.qlref
index 43610d3cc1a5..ccd3827571ee 100644
--- a/java/ql/automodel/test/AutomodelApplicationModeExtraction/AutomodelApplicationModeExtractNegativeExamples.qlref
+++ b/java/ql/automodel/test/AutomodelApplicationModeExtraction/AutomodelApplicationModeExtractNegativeExamples.qlref
@@ -1 +1 @@
-Telemetry/AutomodelApplicationModeExtractNegativeExamples.ql
+AutomodelApplicationModeExtractNegativeExamples.ql
diff --git a/java/ql/automodel/test/AutomodelApplicationModeExtraction/AutomodelApplicationModeExtractPositiveExamples.qlref b/java/ql/automodel/test/AutomodelApplicationModeExtraction/AutomodelApplicationModeExtractPositiveExamples.qlref
index 585a78f94f92..5cf6baa1dba0 100644
--- a/java/ql/automodel/test/AutomodelApplicationModeExtraction/AutomodelApplicationModeExtractPositiveExamples.qlref
+++ b/java/ql/automodel/test/AutomodelApplicationModeExtraction/AutomodelApplicationModeExtractPositiveExamples.qlref
@@ -1 +1 @@
-Telemetry/AutomodelApplicationModeExtractPositiveExamples.ql
+AutomodelApplicationModeExtractPositiveExamples.ql
diff --git a/java/ql/automodel/test/AutomodelFrameworkModeExtraction/AutomodelFrameworkModeExtractCandidates.qlref b/java/ql/automodel/test/AutomodelFrameworkModeExtraction/AutomodelFrameworkModeExtractCandidates.qlref
index e68551eb3ec7..e9b513032aaf 100644
--- a/java/ql/automodel/test/AutomodelFrameworkModeExtraction/AutomodelFrameworkModeExtractCandidates.qlref
+++ b/java/ql/automodel/test/AutomodelFrameworkModeExtraction/AutomodelFrameworkModeExtractCandidates.qlref
@@ -1 +1 @@
-Telemetry/AutomodelFrameworkModeExtractCandidates.ql
+AutomodelFrameworkModeExtractCandidates.ql
diff --git a/java/ql/automodel/test/AutomodelFrameworkModeExtraction/AutomodelFrameworkModeExtractNegativeExamples.qlref b/java/ql/automodel/test/AutomodelFrameworkModeExtraction/AutomodelFrameworkModeExtractNegativeExamples.qlref
index d58a0997fdc5..69498caf8998 100644
--- a/java/ql/automodel/test/AutomodelFrameworkModeExtraction/AutomodelFrameworkModeExtractNegativeExamples.qlref
+++ b/java/ql/automodel/test/AutomodelFrameworkModeExtraction/AutomodelFrameworkModeExtractNegativeExamples.qlref
@@ -1 +1 @@
-Telemetry/AutomodelFrameworkModeExtractNegativeExamples.ql
+AutomodelFrameworkModeExtractNegativeExamples.ql
diff --git a/java/ql/automodel/test/AutomodelFrameworkModeExtraction/AutomodelFrameworkModeExtractPositiveExamples.qlref b/java/ql/automodel/test/AutomodelFrameworkModeExtraction/AutomodelFrameworkModeExtractPositiveExamples.qlref
index ae52dc664968..fbda3f3dd376 100644
--- a/java/ql/automodel/test/AutomodelFrameworkModeExtraction/AutomodelFrameworkModeExtractPositiveExamples.qlref
+++ b/java/ql/automodel/test/AutomodelFrameworkModeExtraction/AutomodelFrameworkModeExtractPositiveExamples.qlref
@@ -1 +1 @@
-Telemetry/AutomodelFrameworkModeExtractPositiveExamples.ql
+AutomodelFrameworkModeExtractPositiveExamples.ql