diff --git a/codan/org.eclipse.cdt.codan.examples/.project b/codan/org.eclipse.cdt.codan.examples/.project
index 7eacfe44864..0fd2e1ce28a 100644
--- a/codan/org.eclipse.cdt.codan.examples/.project
+++ b/codan/org.eclipse.cdt.codan.examples/.project
@@ -20,15 +20,9 @@
 			<arguments>
 			</arguments>
 		</buildCommand>
-		<buildCommand>
-			<name>org.eclipse.pde.api.tools.apiAnalysisBuilder</name>
-			<arguments>
-			</arguments>
-		</buildCommand>
 	</buildSpec>
 	<natures>
 		<nature>org.eclipse.pde.PluginNature</nature>
 		<nature>org.eclipse.jdt.core.javanature</nature>
-		<nature>org.eclipse.pde.api.tools.apiAnalysisNature</nature>
 	</natures>
 </projectDescription>
diff --git a/core/org.eclipse.cdt.core.tests/.project b/core/org.eclipse.cdt.core.tests/.project
index 06a4ddffc04..466f1c10b80 100644
--- a/core/org.eclipse.cdt.core.tests/.project
+++ b/core/org.eclipse.cdt.core.tests/.project
@@ -20,17 +20,11 @@
 			<arguments>
 			</arguments>
 		</buildCommand>
-		<buildCommand>
-			<name>org.eclipse.pde.api.tools.apiAnalysisBuilder</name>
-			<arguments>
-			</arguments>
-		</buildCommand>
 	</buildSpec>
 	<natures>
 		<nature>org.eclipse.jdt.core.javanature</nature>
 		<nature>org.eclipse.pde.PluginNature</nature>
 		<nature>org.eclipse.cdt.core.cnature</nature>
 		<nature>org.eclipse.cdt.core.ccnature</nature>
-		<nature>org.eclipse.pde.api.tools.apiAnalysisNature</nature>
 	</natures>
 </projectDescription>
diff --git a/core/org.eclipse.cdt.core.tests/.settings/.api_filters b/core/org.eclipse.cdt.core.tests/.settings/.api_filters
deleted file mode 100644
index 3015faeefa9..00000000000
--- a/core/org.eclipse.cdt.core.tests/.settings/.api_filters
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8" standalone="no"?>
-<component id="org.eclipse.cdt.core.tests" version="2">
-    <resource path="parser/org/eclipse/cdt/core/parser/tests/scannerinfo/ExtendedScannerInfoSerializerDeserializerTest.java" type="org.eclipse.cdt.core.parser.tests.scannerinfo.ExtendedScannerInfoSerializerDeserializerTest">
-        <filter comment="This is ok - there is just no way of marking @noreference as having friends." id="640712815">
-            <message_arguments>
-                <message_argument value="ExtendedScannerInfo"/>
-                <message_argument value="ExtendedScannerInfoSerializerDeserializerTest"/>
-                <message_argument value="getIncludeExportPatterns()"/>
-            </message_arguments>
-        </filter>
-    </resource>
-</component>
diff --git a/dsf-gdb/org.eclipse.cdt.examples.dsf.gdb/.project b/dsf-gdb/org.eclipse.cdt.examples.dsf.gdb/.project
index 151743cea52..9bcd88e7af4 100644
--- a/dsf-gdb/org.eclipse.cdt.examples.dsf.gdb/.project
+++ b/dsf-gdb/org.eclipse.cdt.examples.dsf.gdb/.project
@@ -20,15 +20,9 @@
 			<arguments>
 			</arguments>
 		</buildCommand>
-		<buildCommand>
-			<name>org.eclipse.pde.api.tools.apiAnalysisBuilder</name>
-			<arguments>
-			</arguments>
-		</buildCommand>
 	</buildSpec>
 	<natures>
 		<nature>org.eclipse.pde.PluginNature</nature>
 		<nature>org.eclipse.jdt.core.javanature</nature>
-		<nature>org.eclipse.pde.api.tools.apiAnalysisNature</nature>
 	</natures>
 </projectDescription>
diff --git a/dsf-gdb/org.eclipse.cdt.tests.dsf.gdb/.project b/dsf-gdb/org.eclipse.cdt.tests.dsf.gdb/.project
index aa2bbf65013..abafad66df8 100644
--- a/dsf-gdb/org.eclipse.cdt.tests.dsf.gdb/.project
+++ b/dsf-gdb/org.eclipse.cdt.tests.dsf.gdb/.project
@@ -30,15 +30,9 @@
 			<arguments>
 			</arguments>
 		</buildCommand>
-		<buildCommand>
-			<name>org.eclipse.pde.api.tools.apiAnalysisBuilder</name>
-			<arguments>
-			</arguments>
-		</buildCommand>
 	</buildSpec>
 	<natures>
 		<nature>org.eclipse.pde.PluginNature</nature>
 		<nature>org.eclipse.jdt.core.javanature</nature>
-		<nature>org.eclipse.pde.api.tools.apiAnalysisNature</nature>
 	</natures>
 </projectDescription>
diff --git a/llvm/org.eclipse.cdt.managedbuilder.llvm.tests/.project b/llvm/org.eclipse.cdt.managedbuilder.llvm.tests/.project
index 4e71adf4dab..333b88b4158 100644
--- a/llvm/org.eclipse.cdt.managedbuilder.llvm.tests/.project
+++ b/llvm/org.eclipse.cdt.managedbuilder.llvm.tests/.project
@@ -20,15 +20,9 @@
 			<arguments>
 			</arguments>
 		</buildCommand>
-		<buildCommand>
-			<name>org.eclipse.pde.api.tools.apiAnalysisBuilder</name>
-			<arguments>
-			</arguments>
-		</buildCommand>
 	</buildSpec>
 	<natures>
 		<nature>org.eclipse.pde.PluginNature</nature>
 		<nature>org.eclipse.jdt.core.javanature</nature>
-		<nature>org.eclipse.pde.api.tools.apiAnalysisNature</nature>
 	</natures>
 </projectDescription>
diff --git a/lsp/org.eclipse.cdt.lsp.cquery/.project b/lsp/org.eclipse.cdt.lsp.cquery/.project
index a7ec13890e7..c758d33fb1f 100644
--- a/lsp/org.eclipse.cdt.lsp.cquery/.project
+++ b/lsp/org.eclipse.cdt.lsp.cquery/.project
@@ -25,15 +25,9 @@
 			<arguments>
 			</arguments>
 		</buildCommand>
-		<buildCommand>
-			<name>org.eclipse.pde.api.tools.apiAnalysisBuilder</name>
-			<arguments>
-			</arguments>
-		</buildCommand>
 	</buildSpec>
 	<natures>
 		<nature>org.eclipse.pde.PluginNature</nature>
 		<nature>org.eclipse.jdt.core.javanature</nature>
-		<nature>org.eclipse.pde.api.tools.apiAnalysisNature</nature>
 	</natures>
 </projectDescription>
diff --git a/releng/scripts/do_project_settings.sh b/releng/scripts/do_project_settings.sh
index c81e091e1d1..bf7d707c2a2 100755
--- a/releng/scripts/do_project_settings.sh
+++ b/releng/scripts/do_project_settings.sh
@@ -98,7 +98,7 @@ git ls-files  -- \*\*/.project | while read i ; do
     natures=$(xmllint --xpath 'string(//projectDescription/natures)' $i)
     if [[ $natures == *"org.eclipse.pde.PluginNature"* ]] && [[ $natures == *"org.eclipse.jdt.core.javanature"* ]]; then
         if [[ $natures != *"org.eclipse.pde.api.tools.apiAnalysisNature"* ]]; then
-            if ! echo $i | grep -E '\.tests?[/\.]' > /dev/null && ! echo $i | grep -E '\.examples?[/\.]' > /dev/null; then
+            if ! echo $i | grep -E '\.tests?[/\.]' > /dev/null && ! echo $i | grep -E '\.examples?[/\.]' > /dev/null && ! echo $i | grep -E 'org.eclipse.cdt.lsp.cquery' > /dev/null; then
                 echo "$d is missing API Tools Nature - Turn it on in Eclipse by 1) Right-click project 2) Plug-in tools -> API Tools Setup"
                 exit 1
             fi
diff --git a/remote/org.eclipse.remote.core.tests/.project b/remote/org.eclipse.remote.core.tests/.project
index 8eccea27b31..1083466962d 100644
--- a/remote/org.eclipse.remote.core.tests/.project
+++ b/remote/org.eclipse.remote.core.tests/.project
@@ -20,15 +20,9 @@
 			<arguments>
 			</arguments>
 		</buildCommand>
-		<buildCommand>
-			<name>org.eclipse.pde.api.tools.apiAnalysisBuilder</name>
-			<arguments>
-			</arguments>
-		</buildCommand>
 	</buildSpec>
 	<natures>
 		<nature>org.eclipse.pde.PluginNature</nature>
 		<nature>org.eclipse.jdt.core.javanature</nature>
-		<nature>org.eclipse.pde.api.tools.apiAnalysisNature</nature>
 	</natures>
 </projectDescription>