Got rid of deprecated usage of manifest Eclipse-AutoStart (changed to LazyStart) and got rid of .project project references because JDT/PDE takes care of these automatically and those are deprecated in the .project file.

plugins/org.eclipse.jem.proxy/.project

diff --git a/plugins/org.eclipse.jem.proxy/.project b/plugins/org.eclipse.jem.proxy/.project
index b820075..0f334e3 100644
--- a/plugins/org.eclipse.jem.proxy/.project
+++ b/plugins/org.eclipse.jem.proxy/.project
@@ -3,12 +3,6 @@
 	<name>org.eclipse.jem.proxy</name>
 	<comment></comment>
 	<projects>
-		<project>org.eclipse.core.resources</project>
-		<project>org.eclipse.core.runtime.compatibility</project>
-		<project>org.eclipse.debug.core</project>
-		<project>org.eclipse.jdt.core</project>
-		<project>org.eclipse.jdt.launching</project>
-		<project>org.eclipse.pde.core</project>
 	</projects>
 	<buildSpec>
 		<buildCommand>

plugins/org.eclipse.jem.proxy/META-INF/MANIFEST.MF

diff --git a/plugins/org.eclipse.jem.proxy/META-INF/MANIFEST.MF b/plugins/org.eclipse.jem.proxy/META-INF/MANIFEST.MF
index 4f105ea..42a16dd 100644
--- a/plugins/org.eclipse.jem.proxy/META-INF/MANIFEST.MF
+++ b/plugins/org.eclipse.jem.proxy/META-INF/MANIFEST.MF
@@ -25,4 +25,4 @@
  org.eclipse.pde.core;resolution:=optional,
  org.eclipse.core.runtime,
  org.eclipse.ui;resolution:=optional
-Eclipse-AutoStart: true
+Eclipse-LazyStart: true

plugins/org.eclipse.jem.ui/.project

diff --git a/plugins/org.eclipse.jem.ui/.project b/plugins/org.eclipse.jem.ui/.project
index aee49c2..71c70e0 100644
--- a/plugins/org.eclipse.jem.ui/.project
+++ b/plugins/org.eclipse.jem.ui/.project
@@ -3,19 +3,6 @@
 	<name>org.eclipse.jem.ui</name>
 	<comment></comment>
 	<projects>
-		<project>org.eclipse.core.resources</project>
-		<project>org.eclipse.core.runtime.compatibility</project>
-		<project>org.eclipse.debug.core</project>
-		<project>org.eclipse.debug.ui</project>
-		<project>org.eclipse.jdt.core</project>
-		<project>org.eclipse.jdt.debug.ui</project>
-		<project>org.eclipse.jdt.launching</project>
-		<project>org.eclipse.jdt.ui</project>
-		<project>org.eclipse.jem.beaninfo</project>
-		<project>org.eclipse.jem.proxy</project>
-		<project>org.eclipse.jem.workbench</project>
-		<project>org.eclipse.ui</project>
-		<project>org.eclipse.ui.ide</project>
 	</projects>
 	<buildSpec>
 		<buildCommand>

plugins/org.eclipse.jem.ui/META-INF/MANIFEST.MF

diff --git a/plugins/org.eclipse.jem.ui/META-INF/MANIFEST.MF b/plugins/org.eclipse.jem.ui/META-INF/MANIFEST.MF
index 652d25d..50fe111 100644
--- a/plugins/org.eclipse.jem.ui/META-INF/MANIFEST.MF
+++ b/plugins/org.eclipse.jem.ui/META-INF/MANIFEST.MF
@@ -24,4 +24,4 @@
  org.eclipse.jem.util,
  org.eclipse.core.runtime,
  org.eclipse.ui.editors
-Eclipse-AutoStart: true
+Eclipse-LazyStart: true