diff --git a/build/org.eclipse.cdt.autotools.docs/.settings/org.eclipse.pde.prefs b/build/org.eclipse.cdt.autotools.docs/.settings/org.eclipse.pde.prefs
index ffaa8e3f1a7..8142f730075 100644
--- a/build/org.eclipse.cdt.autotools.docs/.settings/org.eclipse.pde.prefs
+++ b/build/org.eclipse.cdt.autotools.docs/.settings/org.eclipse.pde.prefs
@@ -2,7 +2,7 @@ compilers.f.unresolved-features=1
 compilers.f.unresolved-plugins=1
 compilers.incompatible-environment=1
 compilers.p.build=1
-compilers.p.build.bin.includes=0
+compilers.p.build.bin.includes=1
 compilers.p.build.encodings=2
 compilers.p.build.java.compiler=2
 compilers.p.build.java.compliance=1
diff --git a/build/org.eclipse.cdt.meson.docs/.settings/org.eclipse.pde.prefs b/build/org.eclipse.cdt.meson.docs/.settings/org.eclipse.pde.prefs
index ffaa8e3f1a7..8142f730075 100644
--- a/build/org.eclipse.cdt.meson.docs/.settings/org.eclipse.pde.prefs
+++ b/build/org.eclipse.cdt.meson.docs/.settings/org.eclipse.pde.prefs
@@ -2,7 +2,7 @@ compilers.f.unresolved-features=1
 compilers.f.unresolved-plugins=1
 compilers.incompatible-environment=1
 compilers.p.build=1
-compilers.p.build.bin.includes=0
+compilers.p.build.bin.includes=1
 compilers.p.build.encodings=2
 compilers.p.build.java.compiler=2
 compilers.p.build.java.compliance=1
diff --git a/debug/org.eclipse.cdt.debug.application.doc/.settings/org.eclipse.pde.prefs b/debug/org.eclipse.cdt.debug.application.doc/.settings/org.eclipse.pde.prefs
index ffaa8e3f1a7..8142f730075 100644
--- a/debug/org.eclipse.cdt.debug.application.doc/.settings/org.eclipse.pde.prefs
+++ b/debug/org.eclipse.cdt.debug.application.doc/.settings/org.eclipse.pde.prefs
@@ -2,7 +2,7 @@ compilers.f.unresolved-features=1
 compilers.f.unresolved-plugins=1
 compilers.incompatible-environment=1
 compilers.p.build=1
-compilers.p.build.bin.includes=0
+compilers.p.build.bin.includes=1
 compilers.p.build.encodings=2
 compilers.p.build.java.compiler=2
 compilers.p.build.java.compliance=1
diff --git a/doc/org.eclipse.cdt.doc.isv/.settings/org.eclipse.pde.prefs b/doc/org.eclipse.cdt.doc.isv/.settings/org.eclipse.pde.prefs
index ffaa8e3f1a7..8142f730075 100644
--- a/doc/org.eclipse.cdt.doc.isv/.settings/org.eclipse.pde.prefs
+++ b/doc/org.eclipse.cdt.doc.isv/.settings/org.eclipse.pde.prefs
@@ -2,7 +2,7 @@ compilers.f.unresolved-features=1
 compilers.f.unresolved-plugins=1
 compilers.incompatible-environment=1
 compilers.p.build=1
-compilers.p.build.bin.includes=0
+compilers.p.build.bin.includes=1
 compilers.p.build.encodings=2
 compilers.p.build.java.compiler=2
 compilers.p.build.java.compliance=1
diff --git a/doc/org.eclipse.cdt.doc.user/.settings/org.eclipse.pde.prefs b/doc/org.eclipse.cdt.doc.user/.settings/org.eclipse.pde.prefs
index ffaa8e3f1a7..8142f730075 100644
--- a/doc/org.eclipse.cdt.doc.user/.settings/org.eclipse.pde.prefs
+++ b/doc/org.eclipse.cdt.doc.user/.settings/org.eclipse.pde.prefs
@@ -2,7 +2,7 @@ compilers.f.unresolved-features=1
 compilers.f.unresolved-plugins=1
 compilers.incompatible-environment=1
 compilers.p.build=1
-compilers.p.build.bin.includes=0
+compilers.p.build.bin.includes=1
 compilers.p.build.encodings=2
 compilers.p.build.java.compiler=2
 compilers.p.build.java.compliance=1
diff --git a/jsoncdb/org.eclipse.cdt.jsoncdb.core.doc/.settings/org.eclipse.pde.prefs b/jsoncdb/org.eclipse.cdt.jsoncdb.core.doc/.settings/org.eclipse.pde.prefs
index ffaa8e3f1a7..8142f730075 100644
--- a/jsoncdb/org.eclipse.cdt.jsoncdb.core.doc/.settings/org.eclipse.pde.prefs
+++ b/jsoncdb/org.eclipse.cdt.jsoncdb.core.doc/.settings/org.eclipse.pde.prefs
@@ -2,7 +2,7 @@ compilers.f.unresolved-features=1
 compilers.f.unresolved-plugins=1
 compilers.incompatible-environment=1
 compilers.p.build=1
-compilers.p.build.bin.includes=0
+compilers.p.build.bin.includes=1
 compilers.p.build.encodings=2
 compilers.p.build.java.compiler=2
 compilers.p.build.java.compliance=1
diff --git a/releng/scripts/do_project_settings.sh b/releng/scripts/do_project_settings.sh
index b4acf5b7760..b4601761532 100755
--- a/releng/scripts/do_project_settings.sh
+++ b/releng/scripts/do_project_settings.sh
@@ -85,6 +85,18 @@ git ls-files  -- \*\*/.project ":!$COREPROJECT/.project" | while read i ; do
                 '-es@compilers.p.not-externalized-att=1@compilers.p.not-externalized-att=2@' \
                 $d/.settings/org.eclipse.pde.prefs
         fi
+        if echo $i | grep -E '\.docs?[/\.]' > /dev/null; then
+            # Docs plug-ins have an index/ directory created at build time
+            sed -i \
+                '-es@compilers.p.build.bin.includes=0@compilers.p.build.bin.includes=1@' \
+                $d/.settings/org.eclipse.pde.prefs
+        fi
+        if echo $i | grep -E 'org.eclipse.remote.proxy.server' > /dev/null; then
+            # Proxy server has a tar file created at build time
+            sed -i \
+                '-es@compilers.p.build.bin.includes=0@compilers.p.build.bin.includes=1@' \
+                $d/.settings/org.eclipse.pde.prefs
+        fi
         if echo $i | grep 'org.eclipse.tm.terminal.view.ui' > /dev/null; then
             # Special case, see comment in org.eclipse.tm.terminal.view.ui/plugin.xml
             sed -i \
diff --git a/remote/org.eclipse.remote.doc.isv/.settings/org.eclipse.pde.prefs b/remote/org.eclipse.remote.doc.isv/.settings/org.eclipse.pde.prefs
index ffaa8e3f1a7..8142f730075 100644
--- a/remote/org.eclipse.remote.doc.isv/.settings/org.eclipse.pde.prefs
+++ b/remote/org.eclipse.remote.doc.isv/.settings/org.eclipse.pde.prefs
@@ -2,7 +2,7 @@ compilers.f.unresolved-features=1
 compilers.f.unresolved-plugins=1
 compilers.incompatible-environment=1
 compilers.p.build=1
-compilers.p.build.bin.includes=0
+compilers.p.build.bin.includes=1
 compilers.p.build.encodings=2
 compilers.p.build.java.compiler=2
 compilers.p.build.java.compliance=1
diff --git a/remote/org.eclipse.remote.proxy.server.core/.settings/org.eclipse.pde.prefs b/remote/org.eclipse.remote.proxy.server.core/.settings/org.eclipse.pde.prefs
index ffaa8e3f1a7..8142f730075 100644
--- a/remote/org.eclipse.remote.proxy.server.core/.settings/org.eclipse.pde.prefs
+++ b/remote/org.eclipse.remote.proxy.server.core/.settings/org.eclipse.pde.prefs
@@ -2,7 +2,7 @@ compilers.f.unresolved-features=1
 compilers.f.unresolved-plugins=1
 compilers.incompatible-environment=1
 compilers.p.build=1
-compilers.p.build.bin.includes=0
+compilers.p.build.bin.includes=1
 compilers.p.build.encodings=2
 compilers.p.build.java.compiler=2
 compilers.p.build.java.compliance=1
diff --git a/remote/org.eclipse.remote.proxy.server.linux.ppc64le/.settings/org.eclipse.pde.prefs b/remote/org.eclipse.remote.proxy.server.linux.ppc64le/.settings/org.eclipse.pde.prefs
index ffaa8e3f1a7..8142f730075 100644
--- a/remote/org.eclipse.remote.proxy.server.linux.ppc64le/.settings/org.eclipse.pde.prefs
+++ b/remote/org.eclipse.remote.proxy.server.linux.ppc64le/.settings/org.eclipse.pde.prefs
@@ -2,7 +2,7 @@ compilers.f.unresolved-features=1
 compilers.f.unresolved-plugins=1
 compilers.incompatible-environment=1
 compilers.p.build=1
-compilers.p.build.bin.includes=0
+compilers.p.build.bin.includes=1
 compilers.p.build.encodings=2
 compilers.p.build.java.compiler=2
 compilers.p.build.java.compliance=1
diff --git a/remote/org.eclipse.remote.proxy.server.linux.x86_64/.settings/org.eclipse.pde.prefs b/remote/org.eclipse.remote.proxy.server.linux.x86_64/.settings/org.eclipse.pde.prefs
index ffaa8e3f1a7..8142f730075 100644
--- a/remote/org.eclipse.remote.proxy.server.linux.x86_64/.settings/org.eclipse.pde.prefs
+++ b/remote/org.eclipse.remote.proxy.server.linux.x86_64/.settings/org.eclipse.pde.prefs
@@ -2,7 +2,7 @@ compilers.f.unresolved-features=1
 compilers.f.unresolved-plugins=1
 compilers.incompatible-environment=1
 compilers.p.build=1
-compilers.p.build.bin.includes=0
+compilers.p.build.bin.includes=1
 compilers.p.build.encodings=2
 compilers.p.build.java.compiler=2
 compilers.p.build.java.compliance=1
diff --git a/remote/org.eclipse.remote.proxy.server.macosx.x86_64/.settings/org.eclipse.pde.prefs b/remote/org.eclipse.remote.proxy.server.macosx.x86_64/.settings/org.eclipse.pde.prefs
index ffaa8e3f1a7..8142f730075 100644
--- a/remote/org.eclipse.remote.proxy.server.macosx.x86_64/.settings/org.eclipse.pde.prefs
+++ b/remote/org.eclipse.remote.proxy.server.macosx.x86_64/.settings/org.eclipse.pde.prefs
@@ -2,7 +2,7 @@ compilers.f.unresolved-features=1
 compilers.f.unresolved-plugins=1
 compilers.incompatible-environment=1
 compilers.p.build=1
-compilers.p.build.bin.includes=0
+compilers.p.build.bin.includes=1
 compilers.p.build.encodings=2
 compilers.p.build.java.compiler=2
 compilers.p.build.java.compliance=1