From 307202b8487a8eef27aaeaceb512afc5a627e691 Mon Sep 17 00:00:00 2001
From: mark <mark@d0ab736e-dc22-4aeb-8dc9-08def0aa14fd>
Date: Wed, 14 Aug 2013 00:02:33 +0000
Subject: [PATCH] New Ant build scripts for Windows.

Work in progress: packaging installer does not yet work.

git-svn-id: https://valelab.ucsf.edu/svn/micromanager2/trunk@11546 d0ab736e-dc22-4aeb-8dc9-08def0aa14fd
---
 acqEngine/build.bat                       |  13 ---
 acqEngine/build.xml                       |  12 +++
 autofocus/build.xml                       | 120 ++++++----------------
 autofocus/buildscripts/Autofocus.xml      |   4 +
 autofocus/buildscripts/AutofocusDuo.xml   |   4 +
 autofocus/buildscripts/AutofocusTB.xml    |   4 +
 autofocus/buildscripts/OughtaFocus.xml    |   4 +
 autofocus/buildscripts/autofocusbuild.xml |  23 +++++
 build.xml                                 | 117 +++++++++++++++++++++
 buildscripts/buildprops.xml               | 104 +++++++++++++++++++
 buildscripts/clojurebuild.xml             |  18 ++++
 buildscripts/javabuild.xml                |  50 +++++++++
 buildscripts/javalibs.xml                 |  24 +++++
 mmstudio/build.xml                        |  47 +++++++++
 mmstudio/build32.bat                      |   2 -
 mmstudio/build32simple.bat                |  47 ---------
 mmstudio/build64.bat                      |   2 -
 plugins/BFCorrector/build.bat             |  17 ---
 plugins/BFCorrector/build.xml             |   3 +
 plugins/Big/build.xml                     |  59 +----------
 plugins/Bleach/build.xml                  |  58 -----------
 plugins/CRISP/build.bat                   |  17 ---
 plugins/CRISP/build.xml                   |   7 ++
 plugins/ClojureEditor/build.xml           |  33 ++----
 plugins/DLLAutoReloader/build.bat         |   7 --
 plugins/DLLAutoReloader/build.xml         |   8 ++
 plugins/DataBrowser/build.bat             |   7 --
 plugins/DataBrowser/build.xml             |   3 +
 plugins/Example/build.xml                 |   3 +
 plugins/Gaussian/build.bat                |  17 ---
 plugins/Gaussian/build.xml                |  13 +++
 plugins/HCS/build.xml                     |  43 +-------
 plugins/ImageFlipper/build.bat            |  17 ---
 plugins/ImageFlipper/build.xml            |   3 +
 plugins/IntelligentAcquisition/build.bat  |  17 ---
 plugins/IntelligentAcquisition/build.xml  |   3 +
 plugins/MetadataExporter/build.xml        |   8 ++
 plugins/MultiCamera/build.xml             |  59 +----------
 plugins/NewImageFlipper/build.bat         |  17 ---
 plugins/NewImageFlipper/build.xml         |   3 +
 plugins/PixelCalibrator/build.xml         |  60 +----------
 plugins/Projector/build.xml               |  62 +----------
 plugins/Recall/build.xml                  |  61 +----------
 plugins/SlideExplorer/build.xml           |  72 ++-----------
 plugins/SlideExplorer2/build.bat          |  12 ---
 plugins/SlideExplorer2/build.xml          |  11 ++
 plugins/SplitView/build.xml               |  61 +----------
 plugins/StageControl/build.xml            |  64 +-----------
 plugins/Tracker/build.xml                 |  58 -----------
 plugins/TwoPhoton/build.xml               |   3 +
 plugins/build.xml                         |  34 ++++++
 plugins/clojurepluginbuild.xml            |   8 ++
 plugins/javapluginbuild.xml               |   8 ++
 plugins/pluginpaths.xml                   |   6 ++
 plugins/pluginprops.xml                   |  11 ++
 55 files changed, 619 insertions(+), 929 deletions(-)
 delete mode 100644 acqEngine/build.bat
 create mode 100644 acqEngine/build.xml
 create mode 100644 autofocus/buildscripts/Autofocus.xml
 create mode 100644 autofocus/buildscripts/AutofocusDuo.xml
 create mode 100644 autofocus/buildscripts/AutofocusTB.xml
 create mode 100644 autofocus/buildscripts/OughtaFocus.xml
 create mode 100644 autofocus/buildscripts/autofocusbuild.xml
 create mode 100644 build.xml
 create mode 100644 buildscripts/buildprops.xml
 create mode 100644 buildscripts/clojurebuild.xml
 create mode 100644 buildscripts/javabuild.xml
 create mode 100644 buildscripts/javalibs.xml
 create mode 100644 mmstudio/build.xml
 delete mode 100644 mmstudio/build32.bat
 delete mode 100644 mmstudio/build32simple.bat
 delete mode 100644 mmstudio/build64.bat
 delete mode 100644 plugins/BFCorrector/build.bat
 create mode 100644 plugins/BFCorrector/build.xml
 delete mode 100644 plugins/Bleach/build.xml
 delete mode 100644 plugins/CRISP/build.bat
 create mode 100644 plugins/CRISP/build.xml
 delete mode 100644 plugins/DLLAutoReloader/build.bat
 create mode 100644 plugins/DLLAutoReloader/build.xml
 delete mode 100644 plugins/DataBrowser/build.bat
 create mode 100644 plugins/DataBrowser/build.xml
 create mode 100644 plugins/Example/build.xml
 delete mode 100644 plugins/Gaussian/build.bat
 create mode 100644 plugins/Gaussian/build.xml
 delete mode 100644 plugins/ImageFlipper/build.bat
 create mode 100644 plugins/ImageFlipper/build.xml
 delete mode 100644 plugins/IntelligentAcquisition/build.bat
 create mode 100644 plugins/IntelligentAcquisition/build.xml
 create mode 100644 plugins/MetadataExporter/build.xml
 delete mode 100644 plugins/NewImageFlipper/build.bat
 create mode 100644 plugins/NewImageFlipper/build.xml
 delete mode 100644 plugins/SlideExplorer2/build.bat
 create mode 100644 plugins/SlideExplorer2/build.xml
 delete mode 100644 plugins/Tracker/build.xml
 create mode 100644 plugins/TwoPhoton/build.xml
 create mode 100644 plugins/build.xml
 create mode 100644 plugins/clojurepluginbuild.xml
 create mode 100644 plugins/javapluginbuild.xml
 create mode 100644 plugins/pluginpaths.xml
 create mode 100644 plugins/pluginprops.xml

diff --git a/acqEngine/build.bat b/acqEngine/build.bat
deleted file mode 100644
index fa5f795779..0000000000
--- a/acqEngine/build.bat
+++ /dev/null
@@ -1,13 +0,0 @@
-if exist classes rmdir classes /s /q
-if exist build rmdir build /s /q
-mkdir classes
-mkdir build
-xcopy /E /y src classes\
-"%JAVA_HOME%\bin\java" -cp ../../3rdpartypublic/classext/clojure.jar;../MMCoreJ_wrap/MMCoreJ.jar;../../3rdpartypublic/classext/ij.jar;../mmstudio/MMJ_.jar;../../3rdpartypublic/classext/bsh-2.0b4.jar;./src -Dclojure.compile.path=classes clojure.lang.Compile org.micromanager.acq-engine
-"%JAVA_HOME%\bin\jar" cf MMAcqEngine.jar -C classes\ .    
-copy /Y MMAcqEngine.jar ..\bin_Win32\
-copy /Y MMAcqEngine.jar ..\bin_x64\
-mkdir ..\Install_Win32\micro-manager\plugins\Micro-Manager
-copy /Y MMAcqEngine.jar ..\Install_Win32\micro-manager\plugins\Micro-Manager\
-mkdir ..\Install_x64\micro-manager\plugins\Micro-Manager
-copy /Y MMAcqEngine.jar ..\Install_x64\micro-manager\plugins\Micro-Manager\
diff --git a/acqEngine/build.xml b/acqEngine/build.xml
new file mode 100644
index 0000000000..0ab45b46de
--- /dev/null
+++ b/acqEngine/build.xml
@@ -0,0 +1,12 @@
+<project name="MMAcqEngine">
+	<property name="namespace" value="org.micromanager.acq-engine"/>
+
+	<import file="../buildscripts/clojurebuild.xml"/>
+
+	<path id="project.classpath">
+		<pathelement location="${mm.java.lib.imagej}"/>
+		<pathelement location="${mm.java.lib.mmcorej}"/>
+		<pathelement location="${mm.java.lib.mmstudio}"/>
+		<pathelement location="${mm.java.lib.beanshell}"/>
+	</path>
+</project>
diff --git a/autofocus/build.xml b/autofocus/build.xml
index da0568efbf..895d4931a7 100644
--- a/autofocus/build.xml
+++ b/autofocus/build.xml
@@ -1,86 +1,34 @@
-<!-- Ant makefile for the Micro-Manager Autofocus plugin  -->
-<!-- This file assumes Micro-Manager project tree structure -->
-
-<project name="Autofocus" default="build">
-
-	<!-- Specify the system path to the ImageJ root directory -->
-	<property name="InstallRoot" value="../Install_AllPlatforms/micro-manager"/>
-
-	<!-- Do not modify from this point on -->
-	<property name="IJ" value="../../3rdpartypublic/classext/ij.jar"/>
-	<property name="beanshell" value="../../3rdpartypublic/classext/bsh-2.0b4.jar"/>
-	<property name="commonsmath" value="../../3rdpartypublic/classext/commons-math-2.0.jar"/>
-          <property name="MMCoreJ" value="../bin_Win32/MMCoreJ.jar"/>
-	<property name="mmautofocus-inst" value="${InstallRoot}/mmautofocus"/>
-	<property name="Runtime" value="../bin_Win32"/>
-
-	<path id="project.class.path">
-		<pathelement location="${IJ}" />
-		<pathelement location="${beanshell}" />
-		<pathelement location="${MMCoreJ}" />
-		<pathelement location="${commonsmath}" />
-	   <pathelement location="../mmstudio/MMJ_.jar"/>
-	</path>
-
-	<target name="compile" description="Compile MM Autofocus plugins.">
-		<mkdir dir="build" />
-		<mkdir dir="buildTB" />
-		<mkdir dir="buildDuo" />
-		<mkdir dir="buildOughta" />
-		<javac srcdir="."  destdir="./build" optimize="on" source="1.5" target="1.5" debug="off">
-			<include name="*.java"/>
-			<exclude name="*TB*.java"/>
-			<exclude name="*Duo*.java"/>
-			<classpath refid="project.class.path" />
-		</javac>
-		<javac srcdir="."  destdir="./buildTB" optimize="on" source="1.5" target="1.5" debug="off">
-			<include name="*TB*.java"/>
-			<exclude name="Autofocus.java"/>
-			<classpath refid="project.class.path" />
-		</javac>
-		<javac srcdir="."  destdir="./buildDuo" optimize="on" source="1.5" target="1.5" debug="off">
-			<include name="*Duo*.java"/>
-			<classpath refid="project.class.path" />
-		</javac>
-		<javac srcdir="."  destdir="./buildOughta" optimize="on" source="1.5" target="1.5" debug="off">
-			<include name="*OughtaFocus*.java"/>
-			<classpath refid="project.class.path" />
-		</javac>
-	</target>
-
-	<target name="build" description="Build MMAutofocus.jar">
-
-		<jar jarfile="MMAutofocus.jar" basedir="build" />
-	
-		<copy file="MMAutofocus.jar" todir="${Runtime}" />
-		<copy file="MMAutofocus.jar" todir="${mmautofocus-inst}/" />
-
-		<jar jarfile="MMAutofocusTB.jar" basedir="buildTB" />
-		
-		<copy file="MMAutofocusTB.jar" todir="${Runtime}" />
-		<copy file="MMAutofocusTB.jar" todir="${mmautofocus-inst}/" />
-	
-		<jar jarfile="MMAutofocusDuo.jar" basedir="buildDuo" />
-		
-		<copy file="MMAutofocusDuo.jar" todir="${Runtime}" />
-		<copy file="MMAutofocusDuo.jar" todir="${mmautofocus-inst}/" />
-
-		<jar jarfile="MMOughtaFocus.jar" basedir="buildOughta" />
-		
-		<copy file="MMOughtaFocus.jar" todir="${Runtime}" />
-		<copy file="MMOughtaFocus.jar" todir="${mmautofocus-inst}/" />
-	</target>
-	
-	<target name="clean" description="Delete the MMAutofocus build files.">
-		<delete dir="build" />
-		<delete file="MMAutofocus.jar" />
-		<delete dir="buildTB" />
-		<delete file="MMAutofocusTB.jar" />
-		<delete dir="buildDuo" />
-		<delete file="MMAutofocusDuo.jar" />
-		<delete dir="buildOughta" />
-		<delete file="MMOughtaFocus.jar" />
-
-	</target>
-	
-</project>
+<project name="mm.autofocus.plugins" basedir="." default="jar">
+	<macrodef name="run-all">
+		<attribute name="target"/>
+		<sequential>
+			<subant target="@{target}">
+				<fileset dir="buildscripts" includes="*.xml" excludes="autofocusbuild.xml"/>
+			</subant>
+		</sequential>
+	</macrodef>
+
+	<target name="prerequisites">
+		<run-all target="prerequisites"/>
+	</target>
+
+	<target name="compile">
+		<run-all target="compile"/>
+	</target>
+
+	<target name="copy-files">
+		<run-all target="copy-files"/>
+	</target>
+
+	<target name="jar">
+		<run-all target="jar"/>
+	</target>
+
+	<target name="install">
+		<run-all target="install"/>
+	</target>
+
+	<target name="clean">
+		<run-all target="clean"/>
+	</target>
+</project>
diff --git a/autofocus/buildscripts/Autofocus.xml b/autofocus/buildscripts/Autofocus.xml
new file mode 100644
index 0000000000..a026586464
--- /dev/null
+++ b/autofocus/buildscripts/Autofocus.xml
@@ -0,0 +1,4 @@
+<project name="MMAutofocus" default="jar">
+	<property name="sourcefile" value="Autofocus.java"/>
+	<import file="autofocusbuild.xml"/>
+</project>
diff --git a/autofocus/buildscripts/AutofocusDuo.xml b/autofocus/buildscripts/AutofocusDuo.xml
new file mode 100644
index 0000000000..fafb98202e
--- /dev/null
+++ b/autofocus/buildscripts/AutofocusDuo.xml
@@ -0,0 +1,4 @@
+<project name="MMAutofocusDuo" default="jar">
+	<property name="sourcefile" value="AutofocusDuo.java"/>
+	<import file="autofocusbuild.xml"/>
+</project>
diff --git a/autofocus/buildscripts/AutofocusTB.xml b/autofocus/buildscripts/AutofocusTB.xml
new file mode 100644
index 0000000000..1aa229d259
--- /dev/null
+++ b/autofocus/buildscripts/AutofocusTB.xml
@@ -0,0 +1,4 @@
+<project name="MMAutofocusTB" default="jar">
+	<property name="sourcefile" value="AutofocusTB.java"/>
+	<import file="autofocusbuild.xml"/>
+</project>
diff --git a/autofocus/buildscripts/OughtaFocus.xml b/autofocus/buildscripts/OughtaFocus.xml
new file mode 100644
index 0000000000..8571952b11
--- /dev/null
+++ b/autofocus/buildscripts/OughtaFocus.xml
@@ -0,0 +1,4 @@
+<project name="MMOughtaFocus" default="jar">
+	<property name="sourcefile" value="OughtaFocus.java"/>
+	<import file="autofocusbuild.xml"/>
+</project>
diff --git a/autofocus/buildscripts/autofocusbuild.xml b/autofocus/buildscripts/autofocusbuild.xml
new file mode 100644
index 0000000000..61ca291ea9
--- /dev/null
+++ b/autofocus/buildscripts/autofocusbuild.xml
@@ -0,0 +1,23 @@
+<project name="mm.autofocusbuild">
+  <include file="../../buildscripts/buildprops.xml"/>
+
+	<property name="srcdir" location=".."/>
+	<property name="installdir" location="${mm.java.autofocus.installdir}"/>
+
+	<import file="../../buildscripts/javabuild.xml"/>
+
+	<path id="project.classpath">
+		<pathelement location="${mm.java.lib.commons-math}"/>
+		<pathelement location="${mm.java.lib.imagej}"/>
+		<pathelement location="${mm.java.lib.mmcorej}"/>
+		<pathelement location="${mm.java.lib.mmstudio}"/>
+	</path>
+
+	<target name="compile" depends="prerequisites" description="Compile Java source">
+		<mkdir dir="${intdir}"/>
+		<mm-javac srcdir="${srcdir}" destdir="${intdir}">
+			<include name="${sourcefile}"/>
+			<classpath refid="project.classpath"/>
+		</mm-javac>
+	</target>
+</project>
diff --git a/build.xml b/build.xml
new file mode 100644
index 0000000000..8c28e757f3
--- /dev/null
+++ b/build.xml
@@ -0,0 +1,117 @@
+<!-- Build all components of Micro-Manager -->
+<!-- Run 'ant -p' for usage -->
+<project name="mm" basedir="." default="build">
+	<include file="buildscripts/buildprops.xml"/>
+
+	<presetdef name="buildcpp">
+		<exec executable="cmd">
+			<arg value="/c"/>
+			<arg value="buildscripts\buildCpp.bat"/>
+			<arg value="${mm.architecture}"/>
+		</exec>
+	</presetdef>
+
+	<target name="build-cpp" description="Build all C++ components">
+		<buildcpp/>
+	</target>
+
+	<target name="build-mmcorej" description="Build MMCoreJ Java package">
+		<!-- Until we update the C++ build and separte out the Java
+		     compilation, just use the results generated by
+		     MMCoreJ_wrap.vcproj -->
+		<mkdir dir="${mm.java.outdir}"/>
+		<copy todir="${mm.java.outdir}" file="${mm.cpp.outdir}/MMCoreJ.jar"/>
+	</target>
+
+	<macrodef name="run-all-java-projects">
+		<attribute name="target"/>
+		<sequential>
+			<subant target="@{target}">
+				<filelist dir=".">
+					<!-- Note: Order matters -->
+					<file name="mmstudio/build.xml"/>
+					<file name="acqEngine/build.xml"/>
+					<file name="plugins/build.xml"/>
+					<file name="autofocus/build.xml"/>
+				</filelist>
+			</subant>
+		</sequential>
+	</macrodef>
+
+	<target name="build" depends="build-cpp,build-mmcorej" description="Build all components">
+		<run-all-java-projects target="jar"/>
+	</target>
+
+	<target name="stage" depends="build" description="Assemble files to install">
+		<run-all-java-projects target="install"/>
+
+		<!-- Until we update the C++ build, just copy all output files
+		     here -->
+		<copy todir="${mm.installdir}">
+			<fileset dir="${mm.cpp.outdir}" includes="*"/>
+		</copy>
+
+		<!-- XXX Remaining files to copy; should put elsewhere -->
+		<copy todir="${mm.installdir}" file="${mm.basedir}/../3rdpartypublic/JavaLauncher/ImageJ.exe"/>
+		<copy todir="${mm.installdir}" file="${mm.java.lib.imagej}"/>
+		<copy todir="${mm.java.installdir}">
+			<!-- XXX Should limit to the Jars that are actually
+			     used. Use Ivy? -->
+			<fileset dir="${mm.java.libs}" includes="*.jar" excludes="ij.jar"/>
+		</copy>
+		<mkdir dir="${mm.scripts.installdir}"/>
+		<copy todir="${mm.scripts.installdir}">
+			<filelist dir="${mm.scripts.srcdir}">
+				<!-- XXX By what criteria are we including scripts? -->
+				<!-- XXX We are out of sync with the Unix build -->
+				<file name="AutoExpose.bsh"/>
+				<file name="Init.bsh"/>
+				<file name="camera_test.bsh"/>
+				<file name="config_test.bsh"/>
+				<file name="image_snap_example.bsh"/>
+				<file name="image_snap_example_2.bsh"/>
+				<file name="live_demo.bsh"/>
+				<file name="manualAcq.bsh"/>
+				<file name="mm_beanshell_startup.bsh"/>
+				<file name="mm_inspector.bsh"/>
+				<file name="mm_load_docs.bsh"/>
+				<file name="mm_test_all.bsh"/>
+				<file name="mm_test_camera.bsh"/>
+				<file name="mm_test_properties.bsh"/>
+				<file name="mm_test_shutter.bsh"/>
+				<file name="mm_test_xystage.bsh"/>
+				<file name="mm_test_zstage.bsh"/>
+				<file name="sdemo1.bsh"/>
+				<file name="sdemo2.bsh"/>
+				<file name="setZoom.bsh"/>
+				<file name="slm_demo.bsh"/>
+			</filelist>
+		</copy>
+	</target>
+
+	<target name="package" depends="stage">
+		<exec dir="${mm.installdir}" executable="${mm.basedir}/../3rdparty/Inno_Setup_5/iscc.exe">
+			<!-- TODO 32 vs 64 -->
+			<arg line="/FMMSetup_ ${mm.basedir}/Install_${mm.architecture}/MM-ImageJ-Install64.iss"/>
+		</exec>
+	</target>
+
+	<target name="clean">
+		<!-- <delete dir="${mm.cpp.outdir}"/> -->
+		<delete dir="${mm.cpp.intdir}"/>
+		<run-all-java-projects target="clean"/>
+	</target>
+
+	<target name="clean-all">
+		<delete dir="${mm.outdir}"/>
+		<delete dir="${mm.intdir}"/>
+	</target>
+
+	<target name="unstage">
+		<delete dir="${mm.installdir}"/>
+	</target>
+
+	<target name="unstage-all">
+		<delete dir="${mm.stagedir}"/>
+	</target>
+</project>
diff --git a/buildscripts/buildprops.xml b/buildscripts/buildprops.xml
new file mode 100644
index 0000000000..54d101694f
--- /dev/null
+++ b/buildscripts/buildprops.xml
@@ -0,0 +1,104 @@
+<project name="mm.props">
+	<!-- Global definitions for building Micro-Manager -->
+
+	<!-- This file should contain property, reference, and macro
+	     definitions but no targets. Everything defined in this file should
+	     have the "mm" prefix. -->
+
+	<!-- Path of repository root, from the project basedir -->
+	<dirname property="mm.basedir" file="${ant.file.mm.props}/.."/>
+
+	<!-- Default build settings; can be overridden on command line -->
+	<!-- TODO Provide reasonable defaults on Unix -->
+	<property name="mm.configuration" value="Release"/>
+	<property name="mm.architecture" value="x64"/>
+
+	<!-- Root of build intermediates directory -->
+	<property name="mm.intdir" location="${mm.basedir}/build/intermediates"/>
+
+	<!-- XXX Override the C++ output dir until we update the Visual Studio
+	     projects -->
+	<property name="mm.cpp.outdir" location="${mm.basedir}/bin_${mm.architecture}"/>
+
+	<!-- Root of build products directory -->
+	<property name="mm.outdir" location="${mm.basedir}/build"/>
+
+	<!-- Root of install/stage directory -->
+	<!-- Unlike the intermediates and products directory, staging can be
+	     configuration/architecture-specific even for platform-independent
+	     (e.g. Java) components. -->
+	<property name="mm.stagedir" location="${mm.basedir}/stage"/>
+	<property name="mm.installdir" location="${mm.stagedir}/${mm.configuration}/${mm.architecture}"/>
+
+	<!-- C++ components -->
+	<property name="mm.cpp.intdir" location="${mm.intdir}/${mm.configuration}/${mm.architecture}"/>
+	<property name="mm.cpp.outdir" location="${mm.outdir}/${mm.configuration}/${mm.architecture}"/>
+
+	<!-- Swig output -->
+	<property name="mm.swig.gensrcdir" location="${mm.intdir}/Swig"/>
+
+	<!-- Java components -->
+	<property name="mm.java.intdir" location="${mm.intdir}/Classes"/>
+	<property name="mm.java.outdir" location="${mm.outdir}/Java"/>
+	<property name="mm.java.installdir" location="${mm.installdir}/plugins/Micro-Manager"/>
+
+	<!-- Java plugins -->
+	<property name="mm.java.plugin.srcdir" location="${mm.basedir}/plugins"/>
+	<property name="mm.java.plugin.intdir" location="${mm.java.intdir}/plugins"/>
+	<property name="mm.java.plugin.outdir" location="${mm.java.outdir}/plugins"/>
+	<property name="mm.java.plugin.installdir" location="${mm.installdir}/mmplugins"/>
+	<property name="mm.java.autofocus.installdir" location="${mm.installdir}/mmautofocus"/>
+
+	<!-- Java library classpaths -->
+	<property name="mm.java.lib.mmcorej" location="${mm.java.outdir}/MMCoreJ.jar"/>
+	<property name="mm.java.lib.mmstudio" location="${mm.java.outdir}/MMJ_.jar"/>
+	<property name="mm.java.lib.acq-engine" location="${mm.java.outdir}/MMAcqEngine.jar"/>
+
+  <!-- Other directories -->
+  <property name="mm.scripts.srcdir" location="${mm.basedir}/scripts"/>
+  <property name="mm.scripts.installdir" location="${mm.installdir}/scripts"/>
+
+	<!-- Third-party lib paths -->
+	<include file="javalibs.xml"/>
+
+	<!-- Packages available by default from plugins -->
+	<path id="mm.java.plugin.defaultclasspath">
+		<pathelement location="${mm.java.lib.commons-math}"/>
+		<pathelement location="${mm.java.lib.imagej}"/>
+		<pathelement location="${mm.java.lib.mmcorej}"/>
+		<pathelement location="${mm.java.lib.mmstudio}"/>
+		<pathelement location="${mm.java.lib.swing-layout}"/>
+	</path>
+
+	<!-- Compiling Java -->
+	<presetdef name="mm-javac">
+		<javac debug="on" debuglevel="lines,vars.source"
+			optimize="on" deprecation="off"
+			source="1.5" target="1.5"
+			includeantruntime="false"/>
+	</presetdef>
+
+	<presetdef name="mm-jar">
+		<jar compress="true" index="true" indexMetaInf="true"/>
+	</presetdef>
+
+	<macrodef name="mm-cljc">
+		<attribute name="namespace"/>
+		<attribute name="srcdir"/>
+		<attribute name="destdir"/>
+		<element name="clj-classpath" optional="false"/>
+		<sequential>
+			<java classname="clojure.lang.Compile" fork="true" failonerror="true">
+				<arg value="@{namespace}"/>
+				<sysproperty key="clojure.compile.path" value="@{destdir}"/>
+				<sysproperty key="java.library.path" value="${mm.cpp.outdir}"/>
+				<classpath>
+					<pathelement location="@{destdir}"/>
+					<pathelement location="@{srcdir}"/>
+					<pathelement location="${mm.java.lib.clojure}"/>
+					<clj-classpath/>
+				</classpath>
+			</java>
+		</sequential>
+	</macrodef>
+</project>
diff --git a/buildscripts/clojurebuild.xml b/buildscripts/clojurebuild.xml
new file mode 100644
index 0000000000..9049bf8837
--- /dev/null
+++ b/buildscripts/clojurebuild.xml
@@ -0,0 +1,18 @@
+<project name="mm.clojurebuild">
+	<!-- This file is intended to be used via 'import' in each Clojure
+	     project's buildfile -->
+
+	<!-- The importing buildfile must define the 'namespace' property -->
+
+	<import file="javabuild.xml"/>
+
+	<!-- Override just the 'compile' target -->
+	<target name="compile" description="Compile Clojure sources">
+		<mkdir dir="${intdir}"/>
+		<mm-cljc namespace="${namespace}" srcdir="${srcdir}" destdir="${intdir}">
+			<clj-classpath>
+				<path refid="project.classpath"/>
+			</clj-classpath>
+		</mm-cljc>
+	</target>
+</project>
diff --git a/buildscripts/javabuild.xml b/buildscripts/javabuild.xml
new file mode 100644
index 0000000000..81042633d8
--- /dev/null
+++ b/buildscripts/javabuild.xml
@@ -0,0 +1,50 @@
+<project name="mm.javabuild">
+	<!-- This file is intended to be used via 'import' in each Java
+	     project's buildfile -->
+
+	<include file="buildprops.xml"/>
+
+	<!-- Default settings (importing buildfile can override) -->
+	<property name="product" value="${ant.project.name}"/>
+	<property name="srcdir" value="src"/>
+	<property name="intdir" location="${mm.java.intdir}/${product}"/>
+	<property name="outdir" location="${mm.java.outdir}"/>
+	<property name="installdir" location="${mm.java.installdir}"/>
+
+	<!-- Settings that are normally not overridden -->
+	<property name="jarfilename" value="${product}.jar"/>
+	<property name="jarfile" value="${outdir}/${product}.jar"/>
+
+	<!-- Default classpath (override after the 'import' element) -->
+	<path id="project.classpath"/>
+
+	<target name="prerequisites" description="Build Jars for prerequisites"/>
+
+	<target name="compile" depends="prerequisites" description="Compile Java sources">
+		<mkdir dir="${intdir}"/>
+		<mm-javac srcdir="${srcdir}" destdir="${intdir}">
+			<classpath refid="project.classpath"/>
+		</mm-javac>
+	</target>
+
+	<target name="copy-files" depends="prerequisites" description="Copy resource files">
+		<copy todir="${intdir}">
+			<fileset dir="${srcdir}" includes="**/*.form"/>
+		</copy>
+	</target>
+
+	<target name="jar" depends="compile,copy-files" description="Build Jar file">
+		<mkdir dir="${outdir}"/>
+		<mm-jar basedir="${intdir}" destfile="${jarfile}"/>
+	</target>
+
+	<target name="install" depends="jar" description="Install Jar file">
+		<mkdir dir="${installdir}"/>
+		<copy todir="${installdir}" file="${jarfile}"/>
+	</target>
+
+	<target name="clean" description="Delete build product and intermediates">
+		<delete file="${jarfile}"/>
+		<delete dir="${intdir}"/>
+	</target>
+</project>
diff --git a/buildscripts/javalibs.xml b/buildscripts/javalibs.xml
new file mode 100644
index 0000000000..75bb75bf33
--- /dev/null
+++ b/buildscripts/javalibs.xml
@@ -0,0 +1,24 @@
+<project name="mm.javalibs">
+	<property name="mm.java.libs" location="${mm.basedir}/../3rdpartypublic/classext"/>
+
+	<!-- Keep alphabetical, please -->
+	<property name="mm.clojure.lib.clooj" location="${mm.java.libs}/clooj.jar"/>
+	<property name="mm.clojure.lib.core-cache" location="${mm.java.libs}/core.cache.jar"/>
+	<property name="mm.clojure.lib.core-memoize" location="${mm.java.libs}/core.memoize.jar"/>
+	<property name="mm.clojure.lib.data-json" location="${mm.java.libs}/data.json.jar"/>
+	<property name="mm.java.lib.beanshell" location="${mm.java.libs}/bsh-2.0b4.jar"/>
+	<property name="mm.java.lib.clojure" location="${mm.java.libs}/clojure.jar"/>
+	<property name="mm.java.lib.commons-math" location="${mm.java.libs}/commons-math-2.0.jar"/>
+	<property name="mm.java.lib.imagej" location="${mm.java.libs}/ij.jar"/>
+	<property name="mm.java.lib.jcommon" location="${mm.java.libs}/jcommon-1.0.16.jar"/>
+	<property name="mm.java.lib.jfreechart" location="${mm.java.libs}/jfreechart-1.0.13.jar"/>
+	<property name="mm.java.lib.loci-common" location="${mm.java.libs}/loci-common.jar"/>
+	<property name="mm.java.lib.ome-xml" location="${mm.java.libs}/ome-xml.jar"/>
+	<property name="mm.java.lib.protobuf" location="${mm.java.libs}/gproto.jar"/>
+	<property name="mm.java.lib.scifio" location="${mm.java.libs}/scifio.jar"/>
+	<property name="mm.java.lib.swing-layout" location="${mm.java.libs}/swing-layout-1.0.4.jar"/>
+	<property name="mm.java.lib.swingx" location="${mm.java.libs}/swingx-0.9.5.jar"/>
+	<property name="mm.java.lib.tsfproto" location="${mm.java.libs}/TSFProto.jar"/>
+
+	<!-- TODO See if at least some of these can be fetched using Ivy -->
+</project>
diff --git a/mmstudio/build.xml b/mmstudio/build.xml
new file mode 100644
index 0000000000..e62f5f74d5
--- /dev/null
+++ b/mmstudio/build.xml
@@ -0,0 +1,47 @@
+<project name="mmstudio" basedir="." default="jar">
+	<!-- Not sure how it got the name "MMJ_", but we'd need significant
+	     planning to change it -->
+	<property name="product" value="MMJ_"/>
+
+	<import file="../buildscripts/javabuild.xml"/>
+
+	<path id="project.classpath">
+		<!-- Keep alphabetical, please -->
+		<pathelement location="${mm.java.lib.beanshell}"/>
+		<pathelement location="${mm.java.lib.commons-math}"/>
+		<pathelement location="${mm.java.lib.imagej}"/>
+		<pathelement location="${mm.java.lib.mmcorej}"/>
+		<pathelement location="${mm.java.lib.scifio}"/>
+		<pathelement location="${mm.java.lib.swing-layout}"/>
+	</path>
+
+	<!-- Override javabuild.xml's 'copy-files' target -->
+	<property name="src.pkgroot" location="${srcdir}/org/micromanager"/>
+	<property name="int.pkgroot" location="${intdir}/org/micromanager"/>
+	<target name="copy-files" depends="mm.javabuild.copy-files">
+		<copy todir="${int.pkgroot}/icons">
+			<fileset dir="${src.pkgroot}/icons">
+				<include name="**/*.png"/>
+				<include name="**/*.gif"/>
+			</fileset>
+		</copy>
+		<copy todir="${int.pkgroot}/conf2">
+			<fileset dir="${src.pkgroot}/conf2" includes="*.html"/>
+		</copy>
+		<copy tofile="${intdir}/plugins.config" file="bin/plugins_mmstudio.config"/>
+	</target>
+
+	<!-- Override javabuild.xml's 'jar' target, to add manifest -->
+	<target name="jar" depends="compile,copy-files">
+		<!-- Note: there is a ${srcdir}/MANIFEST.MF in the repository,
+		     which is probably used by the OS X build. -->
+		<property name="manifest" location="${intdir}/MANIFEST.MF"/>
+		<manifest file="${manifest}">
+			<attribute name="Main-Class" value="org.micromanager.MMStudioMainFrame"/>
+			<!-- TODO Add version information here -->
+		</manifest>
+
+		<mkdir dir="${outdir}"/>
+		<mm-jar basedir="${intdir}" destfile="${jarfile}" manifest="${manifest}"/>
+	</target>
+</project>
diff --git a/mmstudio/build32.bat b/mmstudio/build32.bat
deleted file mode 100644
index 57194c6d69..0000000000
--- a/mmstudio/build32.bat
+++ /dev/null
@@ -1,2 +0,0 @@
-..\..\3rdparty\apache-ant-1.6.5\bin\ant -f build32.xml compile build
-
diff --git a/mmstudio/build32simple.bat b/mmstudio/build32simple.bat
deleted file mode 100644
index 7a7c2ca8ab..0000000000
--- a/mmstudio/build32simple.bat
+++ /dev/null
@@ -1,47 +0,0 @@
-rem Building Micro-Manager 32 bit
-
-rem clean
-rmdir /S/Q build
-del MMJ_.jar
-del MMReader_.jar
-
-rem compile
-md build
-javac -sourcepath ./src -d build -source 1.5 -target 1.5 -g ^
--classpath ../../3rdpartypublic/classext/*;../MMCoreJ_wrap/MMCoreJ.jar; ^
-./src/org/micromanager/utils/AutofocusBase.java
-
-rem copying files
-md build\org\micromanager\icons
-copy /Y src\org\micromanager\icons\*.png build\org\micromanager\icons\
-copy /Y src\org\micromanager\icons\*.gif build\org\micromanager\icons\
-copy /Y src\org\micromanager\conf\*.html build\org\micromanager\conf\
-
-rem make jars
-copy /Y bin\plugins_mmstudio.config build\plugins.config
-jar -cfm MMJ_.jar ./src/MANIFEST.MF -C ./build .
-copy /Y bin\plugins_reader.config build\plugins.config
-jar -cfm MMReader_.jar ./src/MANIFEST.MF -C ./build .
-
-rem install
-del ..\Install_Win32\micro-manager\mmgr_dal_*.dll
-del ..\Install_Win32\micro-manager\MMCoreJ_wrap.dll
-copy /Y ..\DeviceAdapters\TetheredCam\*.dll ..\Install_Win32\micro-manager\
-copy /Y ..\..\3rdpartypublic\classext\data.json.jar ..\Install_Win32\micro-manager\plugins\Micro-Manager\
-move /Y ..\Install_Win32\micro-manager\plugins\ij.jar ..\Install_Win32\micro-manager\
-copy /Y ..\..\3rdpartypublic\JavaLauncher\ImageJ.exe ..\Install_Win32\micro-manager\
-copy /Y MMJ_.jar ..\Install_Win32\micro-manager\
-copy /Y MMJ_.jar ..\bin32\plugins\Micro-Manager\
-copy /Y ..\scripts\*.bsh ..\Install_Win32\micro-manager\scripts\
-copy /Y ..\bin32\mmgr_dal_*.dll ..\Install_Win32\micro-manager\
-copy /Y ..\bin32\MMCoreJ_wrap.dll ..\Install_Win32\micro-manager\
-copy /Y ..\bin32\MMConfig_demo.cfg ..\Install_Win32\micro-manager\
-
-rem Make device list
-java -cp plugins\Micro-Manager\MMJ_.jar;plugins\Micro-Manager\MMCoreJ.jar DeviceListBuilder NotdeviceDiscoveryEnabled
-java -cp plugins\Micro-Manager\MMJ_.jar;plugins\Micro-Manager\MMCoreJ.jar DeviceListBuilder deviceDiscoveryEnabled
-
-rem Create Installation Package
-pushdir ..\Install_Win32\micro-manager\
-..\..\3rdparty\Inno_Setup_5\iscc.exe /F MMSetup_ ../MM-ImageJ-Install32.iss
-popdir
\ No newline at end of file
diff --git a/mmstudio/build64.bat b/mmstudio/build64.bat
deleted file mode 100644
index e8a0f95180..0000000000
--- a/mmstudio/build64.bat
+++ /dev/null
@@ -1,2 +0,0 @@
-..\..\3rdparty\apache-ant-1.6.5\bin\ant -f build64.xml compile build
-
diff --git a/plugins/BFCorrector/build.bat b/plugins/BFCorrector/build.bat
deleted file mode 100644
index 1dffd8708a..0000000000
--- a/plugins/BFCorrector/build.bat
+++ /dev/null
@@ -1,17 +0,0 @@
-rem Build script for BFCorrector plugin
-
-rem clean
-rmdir /S/Q build
-del BFCorrector.jar
-
-rem compile
-md build
-javac -sourcepath ./src -d build -source 1.5 -target 1.5 -g ^
--classpath ../../../3rdpartypublic/classext/*;../../mmstudio/MMJ_.jar;../../MMCoreJ_wrap/MMCoreJ.jar; ^
-./src/org/micromanager/bfcorrector/*.java
-
-rem make jars
-jar cf BFCorrector.jar -C ./build .
-
-rem install
-copy /Y BFCorrector.jar ..\..\Install_AllPlatforms\micro-manager\mmplugins 
\ No newline at end of file
diff --git a/plugins/BFCorrector/build.xml b/plugins/BFCorrector/build.xml
new file mode 100644
index 0000000000..acf63b0a0a
--- /dev/null
+++ b/plugins/BFCorrector/build.xml
@@ -0,0 +1,3 @@
+<project name="BFCorrector" default="jar">
+	<import file="../javapluginbuild.xml"/>
+</project>
diff --git a/plugins/Big/build.xml b/plugins/Big/build.xml
index ff34a8148c..391be18538 100644
--- a/plugins/Big/build.xml
+++ b/plugins/Big/build.xml
@@ -1,58 +1,3 @@
-<!-- Ant makefile for the Micro-Manager Big plugin  -->
-<!-- This file assumes Micro-Manager project tree structure -->
-
-<project name="Big" default="build">
-
-	<!-- Specify the system path to the ImageJ root directory -->
-	<property name="InstallRoot" value="../../Install_AllPlatforms/micro-manager"/>
-
-	<!-- Do not modify from this point on -->
-	<property name="MMPluginDir" value="../../mmstudio"/>
-	<property name="MMCoreJ" value="../../bin_Win32/MMCoreJ.jar"/>
-	<property name="MMPluginsDir-inst" value="${InstallRoot}/mmplugins"/>
-	<property name="BinRoot" value="../../bin_Win32"/>
-        <property name="classext" value="../../../3rdpartypublic/classext"/>
-
-        <property name="IJ" value="${classext}/ij.jar"/>
-        <property name="beanshell" value="${classext}/bsh-2.0b4.jar"/>
-        <property name="swinglayout" value="${classext}/swing-layout-1.0.4.jar"/>
-        <property name="commonsmath" value="${classext}/commons-math-2.0.jar"/>
-        <property name="swingx" value="${classext}/swingx-0.9.5.jar"/>
-
-	<path id="project.MMPlugins.path">
-		<pathelement location="${MMPluginDir}"/>
-	</path>
-
-	<path id="project.class.path">
-		<pathelement location="${MMCoreJ}" />
-		<pathelement location="${MMPluginDir}/MMJ_.jar"/>
-
-		<pathelement location="${IJ}" />
-		<pathelement location="${beanshell}" />
-		<pathelement location="${swinglayout}" />
-		<pathelement location="${commonsmath}" />
-		<pathelement location="${swingx}" />
-
-	</path>
-
-	<target name="compile" description="Compile Big plugin.">
-		<mkdir dir="build" />
-		<javac srcdir="./src" destdir="./build" optimize="on" source="1.5" target="1.5" debug="on">
-			<classpath refid="project.class.path" />
-		</javac>
-		<copy todir="./build/">
-			<fileset dir="./src/" includes="**/*.form" />
-		</copy>
-	</target>
-
-	<target name="build" description="Build Big.jar">
-		<jar jarfile="Big.jar" basedir="build" />
-		<copy file="Big.jar" todir="${MMPluginsDir-inst}" />
-	</target>
-	
-	<target name="clean" description="Delete the Big build files.">
-		<delete dir="build" />
-		<delete file="Big.jar" />
-	</target>
-	
+<project name="Big" default="jar">
+	<import file="../javapluginbuild.xml"/>
 </project>
diff --git a/plugins/Bleach/build.xml b/plugins/Bleach/build.xml
deleted file mode 100644
index 5af5a6ce4e..0000000000
--- a/plugins/Bleach/build.xml
+++ /dev/null
@@ -1,58 +0,0 @@
-<!-- Ant makefile for the Micro-Manager Bleach plugin  -->
-<!-- This file assumes Micro-Manager project tree structure -->
-
-<project name="Bleach" default="build">
-
-	<!-- Specify the system path to the ImageJ root directory -->
-	<property name="InstallRoot" value="../../Install_AllPlatforms/micro-manager"/>
-
-	<!-- Do not modify from this point on -->
-	<property name="MMPluginDir" value="../../mmstudio"/>
-	<property name="MMCoreJ" value="../../bin_Win32/MMCoreJ.jar"/>
-	<property name="MMPluginsDir-inst" value="${InstallRoot}/mmplugins"/>
-	<property name="BinRoot" value="../../bin_Win32"/>
-        <property name="classext" value="../../../3rdpartypublic/classext"/>
-
-        <property name="IJ" value="${classext}/ij.jar"/>
-        <property name="beanshell" value="${classext}/bsh-2.0b4.jar"/>
-        <property name="swinglayout" value="${classext}/swing-layout-1.0.4.jar"/>
-        <property name="commonsmath" value="${classext}/commons-math-2.0.jar"/>
-        <property name="swingx" value="${classext}/swingx-0.9.5.jar"/>
-
-	<path id="project.MMPlugins.path">
-		<pathelement location="${MMPluginDir}"/>
-	</path>
-
-	<path id="project.class.path">
-		<pathelement location="${MMCoreJ}" />
-		<pathelement location="${MMPluginDir}/MMJ_.jar"/>
-
-		<pathelement location="${IJ}" />
-		<pathelement location="${beanshell}" />
-		<pathelement location="${swinglayout}" />
-		<pathelement location="${commonsmath}" />
-		<pathelement location="${swingx}" />
-
-	</path>
-
-	<target name="compile" description="Compile Bleach plugin.">
-		<mkdir dir="build" />
-		<javac srcdir="./src" destdir="./build" optimize="on" source="1.5" target="1.5" debug="on">
-			<classpath refid="project.class.path" />
-		</javac>
-		<copy todir="./build/">
-			<fileset dir="./src/" includes="**/*.form" />
-		</copy>
-	</target>
-
-	<target name="build" description="Build Bleach.jar">
-		<jar jarfile="Bleach.jar" basedir="build" />
-		<copy file="Bleach.jar" todir="${MMPluginsDir-inst}" />
-	</target>
-	
-	<target name="clean" description="Delete the Bleach build files.">
-		<delete dir="build" />
-		<delete file="Bleach.jar" />
-	</target>
-	
-</project>
diff --git a/plugins/CRISP/build.bat b/plugins/CRISP/build.bat
deleted file mode 100644
index 4c8afe58e5..0000000000
--- a/plugins/CRISP/build.bat
+++ /dev/null
@@ -1,17 +0,0 @@
-rem Build script for CRISP plugin
-
-rem clean
-rmdir /S/Q build
-del CRISP.jar
-
-rem compile
-md build
-javac -sourcepath ./src -d build -source 1.5 -target 1.5 -g ^
--classpath ../../../3rdpartypublic/classext/*;../../mmstudio/MMJ_.jar;../../MMCoreJ_wrap/MMCoreJ.jar; ^
-./src/org/micromanager/CRISP/*.java
-
-rem make jars
-jar cf CRISP.jar -C ./build .
-
-rem install
-copy /Y CRISP.jar ..\..\Install_AllPlatforms\micro-manager\mmplugins 
\ No newline at end of file
diff --git a/plugins/CRISP/build.xml b/plugins/CRISP/build.xml
new file mode 100644
index 0000000000..1aed0967f3
--- /dev/null
+++ b/plugins/CRISP/build.xml
@@ -0,0 +1,7 @@
+<project name="CRISP" default="jar">
+	<import file="../javapluginbuild.xml"/>
+
+	<path id="plugin.classpath">
+		<pathelement location="${mm.java.lib.jfreechart}"/>
+	</path>
+</project>
diff --git a/plugins/ClojureEditor/build.xml b/plugins/ClojureEditor/build.xml
index 2c13de3546..4226d06bb0 100644
--- a/plugins/ClojureEditor/build.xml
+++ b/plugins/ClojureEditor/build.xml
@@ -1,29 +1,8 @@
-<!-- Ant makefile for the Micro-Manager ClojureEditor plugin  -->
-<!-- This file assumes Micro-Manager project tree structure -->
+<project name="ClojureEditor" default="jar">
+	<import file="../javapluginbuild.xml"/>
 
-<project name="MMClojureEditor" default="build">
-
-	<target name="compile" description="Compile ClojureEditor plugin.">
-		<mkdir dir="build" />
-		<javac srcdir="./src" destdir="./build" optimize="on" source="1.5" target="1.5" debug="on">
-			<classpath>
-				<pathelement path="../../mmstudio/MMJ_.jar"/>
-				<fileset dir="../../../3rdpartypublic/classext/" >
-					<include name="*.jar"/>
-				</fileset>
-			</classpath>
-
-		</javac>
-	</target>
-
-	<target name="build" description="Build ClojureEditor.jar">
-		<jar jarfile="ClojureEditor.jar" basedir="build" />
-		<copy file="ClojureEditor.jar" todir="..\..\Install_AllPlatforms\micro-manager\mmplugins\" />
-	</target>
-	
-	<target name="clean" description="Delete the ClojureEditor build files.">
-		<delete dir="build" />
-		<delete file="ClojureEditor.jar" />
-	</target>
-	
+	<path id="plugin.classpath">
+		<pathelement location="${mm.java.lib.clojure}"/>
+		<pathelement location="${mm.clojure.lib.clooj}"/>
+	</path>
 </project>
diff --git a/plugins/DLLAutoReloader/build.bat b/plugins/DLLAutoReloader/build.bat
deleted file mode 100644
index 1c9f326953..0000000000
--- a/plugins/DLLAutoReloader/build.bat
+++ /dev/null
@@ -1,7 +0,0 @@
-rem We need Java 6 for this plugin. If you have Java 6, installed, set an environment variable, JDK6, to its location.
-if exist classes rmdir classes /s /q
-mkdir classes
-xcopy /E /y src classes\
-java -cp src;classes;../../../3rdpartypublic/classext/*;../../mmstudio/MMJ_.jar;../../MMCoreJ_wrap/MMCoreJ.jar;../../acqEngine/MMAcqEngine.jar -Djava.library.path=../../bin_x64 -Dclojure.compile.path=classes -server clojure.lang.Compile DLLAutoReloader.plugin
-jar cf DLLAutoReloader.jar -C classes\ .  
-copy /Y DLLAutoReloader.jar ..\..\Install_AllPlatforms\micro-manager\mmplugins\
diff --git a/plugins/DLLAutoReloader/build.xml b/plugins/DLLAutoReloader/build.xml
new file mode 100644
index 0000000000..df5b5d464c
--- /dev/null
+++ b/plugins/DLLAutoReloader/build.xml
@@ -0,0 +1,8 @@
+<project name="DLLAutoReloader" default="jar">
+	<property name="namespace" value="DLLAutoReloader.plugin"/>
+	<import file="../clojurepluginbuild.xml"/>
+	<path id="plugin.classpath">
+		<pathelement location="${mm.java.lib.acq-engine}"/>
+		<pathelement location="${mm.java.lib.beanshell}"/>
+	</path>
+</project>
diff --git a/plugins/DataBrowser/build.bat b/plugins/DataBrowser/build.bat
deleted file mode 100644
index 22a8a33171..0000000000
--- a/plugins/DataBrowser/build.bat
+++ /dev/null
@@ -1,7 +0,0 @@
-rem We need Java 6 for this plugin. If you have Java 6, installed, set an environment variable, JDK6, to its location.
-if exist classes rmdir classes /s /q
-mkdir classes
-xcopy /E /y src classes\
-java -cp src;classes;../../../3rdpartypublic/classext/clojure.jar;../../../3rdpartypublic/classext/data.json.jar;../../../3rdpartypublic/classext/ij.jar;../../../3rdpartypublic/classext/bsh-2.0b4.jar;../../mmstudio/MMJ_.jar;../../MMCoreJ_wrap/MMCoreJ.jar;../../acqEngine/MMAcqEngine.jar -Djava.library.path=../../bin_Win32 -Dclojure.compile.path=classes -server clojure.lang.Compile org.micromanager.browser.plugin
-jar cf DataBrowser.jar -C classes\ .  
-copy /Y DataBrowser.jar ..\..\Install_AllPlatforms\micro-manager\mmplugins\
diff --git a/plugins/DataBrowser/build.xml b/plugins/DataBrowser/build.xml
new file mode 100644
index 0000000000..1f6bd7f0a6
--- /dev/null
+++ b/plugins/DataBrowser/build.xml
@@ -0,0 +1,3 @@
+<project name="DataBrowser" default="jar">
+	<import file="../javapluginbuild.xml"/>
+</project>
diff --git a/plugins/Example/build.xml b/plugins/Example/build.xml
new file mode 100644
index 0000000000..7c96766fc4
--- /dev/null
+++ b/plugins/Example/build.xml
@@ -0,0 +1,3 @@
+<project name="Example" default="jar">
+	<import file="../javapluginbuild.xml"/>
+</project>
diff --git a/plugins/Gaussian/build.bat b/plugins/Gaussian/build.bat
deleted file mode 100644
index 5ed0cd5c0f..0000000000
--- a/plugins/Gaussian/build.bat
+++ /dev/null
@@ -1,17 +0,0 @@
-rem Build script for CRISP plugin
-
-rem clean
-rmdir /S/Q build
-del Gaussian.jar
-
-rem compile
-md build
-javac -sourcepath ./source -d build -source 1.5 -target 1.5 -g ^
--classpath ../../../3rdpartypublic/classext/*;../../mmstudio/MMJ_.jar;../../MMCoreJ_wrap/MMCoreJ.jar; ^
-./source/*.java
-
-rem make jars
-jar cf Gaussian.jar -C ./build .
-
-rem install
-copy /Y Gaussian.jar ..\..\Install_AllPlatforms\micro-manager\mmplugins 
\ No newline at end of file
diff --git a/plugins/Gaussian/build.xml b/plugins/Gaussian/build.xml
new file mode 100644
index 0000000000..47bd3a00e9
--- /dev/null
+++ b/plugins/Gaussian/build.xml
@@ -0,0 +1,13 @@
+<project name="Gaussian" basedir="." default="jar">
+	<!-- TODO Should just move 'source' to 'src' and remove this line -->
+	<property name="srcdir" location="source"/>
+
+	<import file="../javapluginbuild.xml"/>
+
+	<path id="plugin.classpath">
+		<pathelement location="${mm.java.lib.jcommon}"/>
+		<pathelement location="${mm.java.lib.jfreechart}"/>
+		<pathelement location="${mm.java.lib.protobuf}"/>
+		<pathelement location="${mm.java.lib.tsfproto}"/>
+	</path>
+</project>
diff --git a/plugins/HCS/build.xml b/plugins/HCS/build.xml
index 2943da67c3..d4c5816237 100644
--- a/plugins/HCS/build.xml
+++ b/plugins/HCS/build.xml
@@ -1,40 +1,3 @@
-<!-- Ant makefile for the HCS plugin  -->
-<!-- This file assumes Micro-Manager project tree structure -->
-
-<project name="hcs" default="build">
-
-	<!-- Specify the system path to the ImageJ root directory -->
-	<property name="InstallRoot" value="../../Install_AllPlatforms/micro-manager"/>
-
-	<!-- Do not modify from this point on -->
-	<property name="MMCoreJ" value="../../bin_win32/MMCoreJ.jar"/>
-	<property name="MMJ" value="../../mmstudio/MMJ_.jar"/>
-	<property name="MMPluginDir-inst" value="${InstallRoot}/mmplugins"/>
-   <property name="PluginName" value="hcs"/>
-
-	<path id="project.class.path">
-		<pathelement location="${MMCoreJ}" />
-	    <pathelement location="${MMJ}"/>
-	</path>
-
-	<target name="compile" description="Compile HCS plugins.">
-		<mkdir dir="build" />
-		<javac srcdir="." destdir="./build" optimize="on" source="1.5" target="1.5" debug="on">
-			<classpath refid="project.class.path" />
-		</javac>
-	</target>
-
-	<target name="build" description="Build hcs.jar">
-
-		<jar jarfile="${PluginName}.jar" basedir="build" />
-		
-		<mkdir dir="${MMPluginDir-inst}" />
-		<copy file="${PluginName}.jar" todir="${MMPluginDir-inst}/" />
-	</target>
-	
-	<target name="clean" description="Delete the hcs build files.">
-		<delete dir="build" />
-		<delete file="${PluginName}.jar" />
-	</target>
-	
-</project>
\ No newline at end of file
+<project name="HCS" default="jar">
+	<import file="../javapluginbuild.xml"/>
+</project>
diff --git a/plugins/ImageFlipper/build.bat b/plugins/ImageFlipper/build.bat
deleted file mode 100644
index 841a9bee59..0000000000
--- a/plugins/ImageFlipper/build.bat
+++ /dev/null
@@ -1,17 +0,0 @@
-rem Build script for ImageFlipper plugin
-
-rem clean
-rmdir /S/Q build
-del ImageFlipper.jar
-
-rem compile
-md build
-javac -sourcepath ./src -d build -source 1.5 -target 1.5 -g ^
--classpath ../../../3rdpartypublic/classext/*;../../mmstudio/MMJ_.jar;../../MMCoreJ_wrap/MMCoreJ.jar; ^
-./src/org/micromanager/imageflipper/*.java
-
-rem make jars
-jar cf ImageFlipper.jar -C ./build .
-
-rem install
-copy /Y ImageFlipper.jar ..\..\Install_AllPlatforms\micro-manager\mmplugins 
\ No newline at end of file
diff --git a/plugins/ImageFlipper/build.xml b/plugins/ImageFlipper/build.xml
new file mode 100644
index 0000000000..f0be16a336
--- /dev/null
+++ b/plugins/ImageFlipper/build.xml
@@ -0,0 +1,3 @@
+<project name="ImageFlipper" default="jar">
+	<import file="../javapluginbuild.xml"/>
+</project>
diff --git a/plugins/IntelligentAcquisition/build.bat b/plugins/IntelligentAcquisition/build.bat
deleted file mode 100644
index fdd305b864..0000000000
--- a/plugins/IntelligentAcquisition/build.bat
+++ /dev/null
@@ -1,17 +0,0 @@
-rem Build script for IntelligentAcquisition plugin
-
-rem clean
-rmdir /S/Q build
-del IntelligentAcquisition.jar
-
-rem compile
-md build
-javac -sourcepath ./src -d build -source 1.5 -target 1.5 -g ^
--classpath ../../../3rdpartypublic/classext/*;../../mmstudio/MMJ_.jar;../../MMCoreJ_wrap/MMCoreJ.jar; ^
-./src/org/micromanager/intelligentacquisition/*.java
-
-rem make jars
-jar cf IntelligentAcquisition.jar -C ./build .
-
-rem install
-copy /Y IntelligentAcquisition.jar ..\..\Install_AllPlatforms\micro-manager\mmplugins 
\ No newline at end of file
diff --git a/plugins/IntelligentAcquisition/build.xml b/plugins/IntelligentAcquisition/build.xml
new file mode 100644
index 0000000000..25d14147e3
--- /dev/null
+++ b/plugins/IntelligentAcquisition/build.xml
@@ -0,0 +1,3 @@
+<project name="IntelligentAcquisition" default="jar">
+	<import file="../javapluginbuild.xml"/>
+</project>
diff --git a/plugins/MetadataExporter/build.xml b/plugins/MetadataExporter/build.xml
new file mode 100644
index 0000000000..ed0e184116
--- /dev/null
+++ b/plugins/MetadataExporter/build.xml
@@ -0,0 +1,8 @@
+<project name="MetadataExporter" default="jar">
+	<property name="namespace" value="MetadataExporter.core"/>
+	<import file="../clojurepluginbuild.xml"/>
+
+	<path id="plugin.classpath">
+		<pathelement location="${mm.clojure.lib.data-json}"/>
+	</path>
+</project>
diff --git a/plugins/MultiCamera/build.xml b/plugins/MultiCamera/build.xml
index 5bd6b8d4a7..99e9703086 100644
--- a/plugins/MultiCamera/build.xml
+++ b/plugins/MultiCamera/build.xml
@@ -1,58 +1,3 @@
-<!-- Ant makefile for the Micro-Manager MultiCamera plugin  -->
-<!-- This file assumes Micro-Manager project tree structure -->
-
-<project name="MultiCamera" default="build">
-
-	<!-- Specify the system path to the ImageJ root directory -->
-	<property name="InstallRoot" value="../../Install_AllPlatforms/micro-manager"/>
-
-	<!-- Do not modify from this point on -->
-	<property name="MMPluginDir" value="../../mmstudio"/>
-	<property name="MMCoreJ" value="../../bin_Win32/MMCoreJ.jar"/>
-	<property name="MMPluginsDir-inst" value="${InstallRoot}/mmplugins"/>
-	<property name="BinRoot" value="../../bin_Win32"/>
-        <property name="classext" value="../../../3rdpartypublic/classext"/>
-
-        <property name="IJ" value="${classext}/ij.jar"/>
-        <property name="beanshell" value="${classext}/bsh-2.0b4.jar"/>
-        <property name="swinglayout" value="${classext}/swing-layout-1.0.4.jar"/>
-        <property name="commonsmath" value="${classext}/commons-math-2.0.jar"/>
-        <property name="swingx" value="${classext}/swingx-0.9.5.jar"/>
-
-	<path id="project.MMPlugins.path">
-		<pathelement location="${MMPluginDir}"/>
-	</path>
-
-	<path id="project.class.path">
-		<pathelement location="${MMCoreJ}" />
-		<pathelement location="${MMPluginDir}/MMJ_.jar"/>
-
-		<pathelement location="${IJ}" />
-		<pathelement location="${beanshell}" />
-		<pathelement location="${swinglayout}" />
-		<pathelement location="${commonsmath}" />
-		<pathelement location="${swingx}" />
-
-	</path>
-
-	<target name="compile" description="Compile MultiCamera plugin.">
-		<mkdir dir="build" />
-		<javac srcdir="./src" destdir="./build" optimize="on" source="1.5" target="1.5" debug="on">
-			<classpath refid="project.class.path" />
-		</javac>
-		<copy todir="./build/">
-			<fileset dir="./src/" includes="**/*.form" />
-		</copy>
-	</target>
-
-	<target name="build" description="Build MultiCamera.jar">
-		<jar jarfile="MultiCamera.jar" basedir="build" />
-		<copy file="MultiCamera.jar" todir="${MMPluginsDir-inst}" />
-	</target>
-	
-	<target name="clean" description="Delete the MultiCamera build files.">
-		<delete dir="build" />
-		<delete file="MultiCamera.jar" />
-	</target>
-	
+<project name="MultiCamera" default="jar">
+	<import file="../javapluginbuild.xml"/>
 </project>
diff --git a/plugins/NewImageFlipper/build.bat b/plugins/NewImageFlipper/build.bat
deleted file mode 100644
index 2c1d5d7b45..0000000000
--- a/plugins/NewImageFlipper/build.bat
+++ /dev/null
@@ -1,17 +0,0 @@
-rem Build script for ImageFlipper plugin
-
-rem clean
-rmdir /S/Q build
-del ImageFlipper.jar
-
-rem compile
-md build
-javac -sourcepath ./src -d build -source 1.5 -target 1.5 -g ^
--classpath ../../../3rdpartypublic/classext/*;../../mmstudio/MMJ_.jar;../../MMCoreJ_wrap/MMCoreJ.jar; ^
-./src/org/micromanager/newimageflipper/*.java
-
-rem make jars
-jar cf ImageFlipper.jar -C ./build .
-
-rem install
-copy /Y ImageFlipper.jar ..\..\Install_AllPlatforms\micro-manager\mmplugins 
\ No newline at end of file
diff --git a/plugins/NewImageFlipper/build.xml b/plugins/NewImageFlipper/build.xml
new file mode 100644
index 0000000000..88019b39b9
--- /dev/null
+++ b/plugins/NewImageFlipper/build.xml
@@ -0,0 +1,3 @@
+<project name="NewImageFlipper" default="jar">
+	<import file="../javapluginbuild.xml"/>
+</project>
diff --git a/plugins/PixelCalibrator/build.xml b/plugins/PixelCalibrator/build.xml
index 4023cd035f..ebddb996f1 100755
--- a/plugins/PixelCalibrator/build.xml
+++ b/plugins/PixelCalibrator/build.xml
@@ -1,57 +1,3 @@
-<!-- Ant makefile for the Micro-Manager PixelCalibrator plugin  -->
-<!-- This file assumes Micro-Manager project tree structure -->
-
-<project name="MMPixelCalibrator" default="build">
-
-	<!-- Specify the system path to the ImageJ root directory -->
-	<property name="InstallRoot" value="../../Install_AllPlatforms/micro-manager"/>
-
-	<!-- Do not modify from this point on -->
-	<property name="MMPluginDir" value="../../mmstudio"/>
-	<property name="MMCoreJ" value="../../bin_Win32/MMCoreJ.jar"/>
-	<property name="MMPluginsDir-inst" value="${InstallRoot}/mmplugins"/>
-	<property name="BinRoot" value="../../bin_Win32"/>
-        <property name="classext" value="../../../3rdpartypublic/classext"/>
-
-	<property name="IJ" value="${classext}/ij.jar"/>
-	<property name="beanshell" value="${classext}/bsh-2.0b4.jar"/>
-	<property name="swinglayout" value="${classext}/swing-layout-1.0.4.jar"/>
-	<property name="commonsmath" value="${classext}/commons-math-2.0.jar"/>
-	<property name="swingx" value="${classext}/swingx-0.9.5.jar"/>
-
-
-	<path id="project.MMPlugins.path">
-		<pathelement location="${MMPluginDir}"/>
-	</path>
-
-	<path id="project.class.path">
-		<pathelement location="${MMCoreJ}" />
-		<pathelement location="${MMPluginDir}/MMJ_.jar"/>
-
-		<pathelement location="${IJ}" />
-		<pathelement location="${beanshell}" />
-		<pathelement location="${swinglayout}" />
-		<pathelement location="${commonsmath}" />
-		<pathelement location="${swingx}" />
-
-	</path>
-
-	<target name="compile" description="Compile PixelCalibrator plugin.">
-		<mkdir dir="build" />
-		<javac srcdir="./src" destdir="./build" optimize="on" source="1.5" target="1.5" debug="on">
-			<classpath refid="project.class.path" />
-		</javac>
-		<copy file="./src/org/micromanager/pixelcalibrator/PixelCalibratorDialog.form" todir="./build/org/micromanager/pixelcalibrator/" />
-	</target>
-
-	<target name="build" description="Build PixelCalibrator.jar">
-		<jar jarfile="PixelCalibrator.jar" basedir="build" />
-		<copy file="PixelCalibrator.jar" todir="${MMPluginsDir-inst}" />
-	</target>
-	
-	<target name="clean" description="Delete the PixelCalibrator build files.">
-		<delete dir="build" />
-		<delete file="PixelCalibrator.jar" />
-	</target>
-	
-</project>
+<project name="PixelCalibrator" default="jar">
+	<import file="../javapluginbuild.xml"/>
+</project>
diff --git a/plugins/Projector/build.xml b/plugins/Projector/build.xml
index 49d132aa26..ae2d64910c 100755
--- a/plugins/Projector/build.xml
+++ b/plugins/Projector/build.xml
@@ -1,59 +1,3 @@
-<!-- Ant makefile for the Micro-Manager Projector plugin  -->
-<!-- This file assumes Micro-Manager project tree structure -->
-
-<project name="MMProjector" default="build">
-
-	<!-- Specify the system path to the ImageJ root directory -->
-	<property name="InstallRoot" value="../../Install_AllPlatforms/micro-manager"/>
-
-	<!-- Do not modify from this point on -->
-	<property name="MMPluginDir" value="../../bin_Win32/plugins/Micro-Manager"/>
-	<property name="MMCoreJ" value="../../bin_Win32/MMCoreJ.jar"/>
-	<property name="MMPluginsDir-inst" value="${InstallRoot}/mmplugins"/>
-	<property name="BinRoot" value="../../bin_Win32"/>
-        <property name="classext" value="../../../3rdpartypublic/classext"/>
-
-        <property name="IJ" value="${classext}/ij.jar"/>
-        <property name="beanshell" value="${classext}/bsh-2.0b4.jar"/>
-        <property name="swinglayout" value="${classext}/swing-layout-1.0.4.jar"/>
-        <property name="commonsmath" value="${classext}/commons-math-2.0.jar"/>
-        <property name="swingx" value="${classext}/swingx-0.9.5.jar"/>
-
-	<path id="project.MMPlugins.path">
-		<pathelement location="${MMPluginDir}"/>
-	</path>
-
-	<path id="project.class.path">
-		<pathelement location="${MMCoreJ}" />
-		<pathelement location="${MMPluginDir}/MMJ_.jar"/>
-
-		<pathelement location="${IJ}" />
-		<pathelement location="${beanshell}" />
-		<pathelement location="${swinglayout}" />
-		<pathelement location="${commonsmath}" />
-		<pathelement location="${swingx}" />
-		
-
-	</path>
-
-	<target name="compile" description="Compile Projector plugin.">
-		<mkdir dir="build" />
-		<javac srcdir="./src" destdir="./build" optimize="on" source="1.5" target="1.5" debug="on">
-			<classpath refid="project.class.path" />
-		</javac>
-		<copy todir="./build/">
-			<fileset dir="./src/" includes="**/*.form" />
-		</copy>
-	</target>
-
-	<target name="build" description="Build projector.jar">
-		<jar jarfile="projector.jar" basedir="build" />
-		<copy file="projector.jar" todir="${MMPluginsDir-inst}" />
-	</target>
-	
-	<target name="clean" description="Delete the Projector build files.">
-		<delete dir="build" />
-		<delete file="projector.jar" />
-	</target>
-	
-</project>
+<project name="Projector" default="jar">
+	<import file="../javapluginbuild.xml"/>
+</project>
diff --git a/plugins/Recall/build.xml b/plugins/Recall/build.xml
index 725518b6b4..9f918a8a95 100644
--- a/plugins/Recall/build.xml
+++ b/plugins/Recall/build.xml
@@ -1,58 +1,3 @@
-<!-- Ant makefile for the Micro-Manager Recall plugin  -->
-<!-- This file assumes Micro-Manager project tree structure -->
-
-<project name="Recall" default="build">
-
-	<!-- Specify the system path to the ImageJ root directory -->
-	<property name="InstallRoot" value="../../Install_AllPlatforms/micro-manager"/>
-
-	<!-- Do not modify from this point on -->
-	<property name="MMPluginDir" value="../../mmstudio"/>
-	<property name="MMCoreJ" value="../../bin_Win32/MMCoreJ.jar"/>
-	<property name="MMPluginsDir-inst" value="${InstallRoot}/mmplugins"/>
-	<property name="BinRoot" value="../../bin_Win32"/>
-        <property name="classext" value="../../../3rdpartypublic/classext"/>
-
-        <property name="IJ" value="${classext}/ij.jar"/>
-        <property name="beanshell" value="${classext}/bsh-2.0b4.jar"/>
-        <property name="swinglayout" value="${classext}/swing-layout-1.0.4.jar"/>
-        <property name="commonsmath" value="${classext}/commons-math-2.0.jar"/>
-        <property name="swingx" value="${classext}/swingx-0.9.5.jar"/>
-
-	<path id="project.MMPlugins.path">
-		<pathelement location="${MMPluginDir}"/>
-	</path>
-
-	<path id="project.class.path">
-		<pathelement location="${MMCoreJ}" />
-		<pathelement location="${MMPluginDir}/MMJ_.jar"/>
-
-		<pathelement location="${IJ}" />
-		<pathelement location="${beanshell}" />
-		<pathelement location="${swinglayout}" />
-		<pathelement location="${commonsmath}" />
-		<pathelement location="${swingx}" />
-
-	</path>
-
-	<target name="compile" description="Compile Recall plugin.">
-		<mkdir dir="build" />
-		<javac srcdir="./src" destdir="./build" optimize="on" source="1.5" target="1.5" debug="on">
-			<classpath refid="project.class.path" />
-		</javac>
-		<copy todir="./build/">
-			<fileset dir="./src/" includes="**/*.form" />
-		</copy>
-	</target>
-
-	<target name="build" description="Build Recall.jar">
-		<jar jarfile="Recall.jar" basedir="build" />
-		<copy file="Recall.jar" todir="${MMPluginsDir-inst}" />
-	</target>
-	
-	<target name="clean" description="Delete the Recall build files.">
-		<delete dir="build" />
-		<delete file="Recall.jar" />
-	</target>
-	
-</project>
+<project name="Recall" default="jar">
+	<import file="../javapluginbuild.xml"/>
+</project>
diff --git a/plugins/SlideExplorer/build.xml b/plugins/SlideExplorer/build.xml
index ac240c3721..bc1e423b79 100755
--- a/plugins/SlideExplorer/build.xml
+++ b/plugins/SlideExplorer/build.xml
@@ -1,61 +1,11 @@
-<!-- Ant makefile for the Micro-Manager SlideExplorer plugin  -->
-<!-- This file assumes Micro-Manager project tree structure -->
-
-<project name="MMSlideExplorer" default="build">
-
-	<!-- Specify the system path to the ImageJ root directory -->
-	<property name="InstallRoot" value="../../Install_AllPlatforms/micro-manager"/>
-
-	<!-- Do not modify from this point on -->
-	<property name="MMPluginDir" value="../../mmstudio"/>
-	<property name="MMCoreJ" value="../../bin_Win32/MMCoreJ.jar"/>
-	<property name="MMPluginsDir-inst" value="${InstallRoot}/mmplugins"/>
-	<property name="BinRoot" value="../../bin_Win32"/>
-    <property name="classext" value="../../../3rdpartypublic/classext"/>
-
-        <property name="IJ" value="${classext}/ij.jar"/>
-        <property name="beanshell" value="${classext}/bsh-2.0b4.jar"/>
-        <property name="swinglayout" value="${classext}/swing-layout-1.0.4.jar"/>
-        <property name="commonsmath" value="${classext}/commons-math-2.0.jar"/>
-        <property name="swingx" value="${classext}/swingx-0.9.5.jar"/>
-
-	<property name="pixelcalibrator" value="../PixelCalibrator/PixelCalibrator.jar"/>
-
-	<path id="project.MMPlugins.path">
-		<pathelement location="${MMPluginDir}"/>
-	</path>
-
-	<path id="project.class.path">
-		<pathelement location="${MMCoreJ}" />
-		<pathelement location="${MMPluginDir}/MMJ_.jar"/>
-
-		<pathelement location="${IJ}" />
-		<pathelement location="${beanshell}" />
-		<pathelement location="${swinglayout}" />
-		<pathelement location="${commonsmath}" />
-		<pathelement location="${swingx}" />
-		<pathelement location="${pixelcalibrator}" />
-
-	</path>
-
-	<target name="compile" description="Compile SlideExplorer plugin.">
-		<mkdir dir="build" />
-		<javac srcdir="./src" destdir="./build" optimize="on" source="1.5" target="1.5" debug="on">
-			<classpath refid="project.class.path" />
-		</javac>
-		<copy todir="./build/">
-			<fileset dir="./src/" includes="**/*.form" />
-		</copy>
-	</target>
-
-	<target name="build" description="Build SlideExplorer.jar">
-		<jar jarfile="SlideExplorer.jar" basedir="build" />
-		<copy file="SlideExplorer.jar" todir="${MMPluginsDir-inst}" />
-	</target>
-	
-	<target name="clean" description="Delete the SlideExplorer build files.">
-		<delete dir="build" />
-		<delete file="SlideExplorer.jar" />
-	</target>
-	
-</project>
+<project name="SlideExplorer" default="jar">
+	<import file="../javapluginbuild.xml"/>
+
+	<path id="plugin.classpath">
+		<pathelement location="${mm.java.plugin.outdir}/PixelCalibrator.jar"/>
+	</path>
+
+	<target name="prerequisites" depends="mm.javabuild.prerequisites">
+		<ant dir="../PixelCalibrator" target="jar" inheritAll="false" useNativeBasedir="true"/>
+	</target>
+</project>
diff --git a/plugins/SlideExplorer2/build.bat b/plugins/SlideExplorer2/build.bat
deleted file mode 100644
index 6dc2b694a8..0000000000
--- a/plugins/SlideExplorer2/build.bat
+++ /dev/null
@@ -1,12 +0,0 @@
-rem We need Java 6 for this plugin. If you have Java 6, installed, set an environment variable, JDK6, to its location.
-if exist classes rmdir classes /s /q
-if exist build rmdir build /s /q
-mkdir classes
-mkdir build
-mkdir 
-xcopy /E /y src classes\
-java -cp src;classes;../../../3rdpartypublic/classext/clojure.jar;../../../3rdpartypublic/classext/core.cache.jar;../../../3rdpartypublic/classext/core.memoize.jar;../../../3rdpartypublic/classext/ij.jar;../../../3rdpartypublic/classext/bsh-2.0b4.jar;../../mmstudio/MMJ_.jar;../../MMCoreJ_wrap/MMCoreJ.jar;../../acqEngine/MMAcqEngine.jar -Djava.library.path=../../bin_x64 -Dclojure.compile.path=classes -server clojure.lang.Compile slide-explorer.plugin
-xcopy /E /y src build\
-xcopy classes\org\micromanager\SlideExplorer2.class build\org\micromanager\
-jar cf SlideExplorer2.jar -C build\ .  
-copy /Y SlideExplorer2.jar ..\..\Install_AllPlatforms\micro-manager\mmplugins\
diff --git a/plugins/SlideExplorer2/build.xml b/plugins/SlideExplorer2/build.xml
new file mode 100644
index 0000000000..5e327db6a7
--- /dev/null
+++ b/plugins/SlideExplorer2/build.xml
@@ -0,0 +1,11 @@
+<project name="SlideExplorer2" default="jar">
+	<property name="namespace" value="slide-explorer.plugin"/>
+	<import file="../clojurepluginbuild.xml"/>
+
+	<path id="plugin.classpath">
+		<pathelement location="${mm.java.lib.acq-engine}"/>
+		<pathelement location="${mm.java.lib.beanshell}"/>
+		<pathelement location="${mm.clojure.lib.core-cache}"/>
+		<pathelement location="${mm.clojure.lib.core-memoize}"/>
+	</path>
+</project>
diff --git a/plugins/SplitView/build.xml b/plugins/SplitView/build.xml
index edbd29b589..7f4426973d 100644
--- a/plugins/SplitView/build.xml
+++ b/plugins/SplitView/build.xml
@@ -1,58 +1,3 @@
-<!-- Ant makefile for the Micro-Manager SplitView plugin  -->
-<!-- This file assumes Micro-Manager project tree structure -->
-
-<project name="SplitView" default="build">
-
-	<!-- Specify the system path to the ImageJ root directory -->
-	<property name="InstallRoot" value="../../Install_AllPlatforms/micro-manager"/>
-
-	<!-- Do not modify from this point on -->
-	<property name="MMPluginDir" value="../../mmstudio"/>
-	<property name="MMCoreJ" value="../../bin_Win32/MMCoreJ.jar"/>
-	<property name="MMPluginsDir-inst" value="${InstallRoot}/mmplugins"/>
-	<property name="BinRoot" value="../../bin_Win32"/>
-        <property name="classext" value="../../../3rdpartypublic/classext"/>
-
-        <property name="IJ" value="${classext}/ij.jar"/>
-        <property name="beanshell" value="${classext}/bsh-2.0b4.jar"/>
-        <property name="swinglayout" value="${classext}/swing-layout-1.0.4.jar"/>
-        <property name="commonsmath" value="${classext}/commons-math-2.0.jar"/>
-        <property name="swingx" value="${classext}/swingx-0.9.5.jar"/>
-
-	<path id="project.MMPlugins.path">
-		<pathelement location="${MMPluginDir}"/>
-	</path>
-
-	<path id="project.class.path">
-		<pathelement location="${MMCoreJ}" />
-		<pathelement location="${MMPluginDir}/MMJ_.jar"/>
-
-		<pathelement location="${IJ}" />
-		<pathelement location="${beanshell}" />
-		<pathelement location="${swinglayout}" />
-		<pathelement location="${commonsmath}" />
-		<pathelement location="${swingx}" />
-
-	</path>
-
-	<target name="compile" description="Compile SplitView plugin.">
-		<mkdir dir="build" />
-		<javac srcdir="./src" destdir="./build" optimize="on" source="1.5" target="1.5" debug="on">
-			<classpath refid="project.class.path" />
-		</javac>
-		<copy todir="./build/">
-			<fileset dir="./src/" includes="**/*.form" />
-		</copy>
-	</target>
-
-	<target name="build" description="Build SplitView.jar">
-		<jar jarfile="SplitView.jar" basedir="build" />
-		<copy file="SplitView.jar" todir="${MMPluginsDir-inst}" />
-	</target>
-	
-	<target name="clean" description="Delete the SplitView build files.">
-		<delete dir="build" />
-		<delete file="SplitView.jar" />
-	</target>
-	
-</project>
+<project name="SplitView" default="jar">
+	<import file="../javapluginbuild.xml"/>
+</project>
diff --git a/plugins/StageControl/build.xml b/plugins/StageControl/build.xml
index 21481253d4..39cad4e32f 100644
--- a/plugins/StageControl/build.xml
+++ b/plugins/StageControl/build.xml
@@ -1,61 +1,3 @@
-<!-- Ant makefile for the Micro-Manager StageControl plugin  -->
-<!-- This file assumes Micro-Manager project tree structure -->
-
-<project name="StageControl" default="build">
-
-	<!-- Specify the system path to the ImageJ root directory -->
-	<property name="InstallRoot" value="../../Install_AllPlatforms/micro-manager"/>
-
-	<!-- Do not modify from this point on -->
-	<property name="MMPluginDir" value="../../mmstudio"/>
-	<property name="MMCoreJ" value="../../bin_Win32/MMCoreJ.jar"/>
-	<property name="MMPluginsDir-inst" value="${InstallRoot}/mmplugins"/>
-	<property name="BinRoot" value="../../bin_Win32"/>
-   <property name="classext" value="../../../3rdpartypublic/classext"/>
-
-	<property name="IJ" value="${classext}/ij.jar"/>
-	<property name="beanshell" value="${classext}/bsh-2.0b4.jar"/>
-	<property name="swinglayout" value="${classext}/swing-layout-1.0.4.jar"/>
-	<property name="commonsmath" value="${classext}/commons-math-2.0.jar"/>
-	<property name="swingx" value="${classext}/swingx-0.9.5.jar"/>
-
-
-	<path id="project.MMPlugins.path">
-		<pathelement location="${MMPluginDir}"/>
-	</path>
-
-	<path id="project.class.path">
-		<pathelement location="${MMCoreJ}" />
-		<pathelement location="${MMPluginDir}/MMJ_.jar"/>
-
-		<pathelement location="${IJ}" />
-		<pathelement location="${beanshell}" />
-		<pathelement location="${swinglayout}" />
-		<pathelement location="${commonsmath}" />
-		<pathelement location="${swingx}" />
-
-	</path>
-
-	<target name="compile" description="Compile StageControl plugin.">
-		<mkdir dir="build" />
-		<javac srcdir="./src" destdir="./build" optimize="on" source="1.5" target="1.5" debug="on">
-			<classpath refid="project.class.path" />
-		</javac>
-		<copy file="./src/org/micromanager/stagecontrol/StageControlFrame.form" todir="./build/org/micromanager/stagecontrol/" />
-	   <copy todir="./build/org/micromanager/stagecontrol/icons">
-	       <fileset dir="./src/org/micromanager/stagecontrol/icons" includes="*.*" />
-	   </copy>
-
-	</target>
-
-	<target name="build" description="Build StageControl.jar">
-		<jar jarfile="StageControl.jar" basedir="build" />
-		<copy file="StageControl.jar" todir="${MMPluginsDir-inst}" />
-	</target>
-	
-	<target name="clean" description="Delete the StageControl build files.">
-		<delete dir="build" />
-		<delete file="StageControl.jar" />
-	</target>
-	
-</project>
+<project name="StageControl" default="jar">
+	<import file="../javapluginbuild.xml"/>
+</project>
diff --git a/plugins/Tracker/build.xml b/plugins/Tracker/build.xml
deleted file mode 100644
index 205ab99f3a..0000000000
--- a/plugins/Tracker/build.xml
+++ /dev/null
@@ -1,58 +0,0 @@
-<!-- Ant makefile for the Micro-Manager Recall plugin  -->
-<!-- This file assumes Micro-Manager project tree structure -->
-
-<project name="Tracker" default="build">
-
-	<!-- Specify the system path to the ImageJ root directory -->
-	<property name="InstallRoot" value="../../Install_AllPlatforms/micro-manager"/>
-
-	<!-- Do not modify from this point on -->
-	<property name="MMPluginDir" value="../../mmstudio"/>
-	<property name="MMCoreJ" value="../../bin_Win32/MMCoreJ.jar"/>
-	<property name="MMPluginsDir-inst" value="${InstallRoot}/mmplugins"/>
-	<property name="BinRoot" value="../../bin_Win32"/>
-        <property name="classext" value="../../../3rdpartypublic/classext"/>
-
-        <property name="IJ" value="${classext}/ij.jar"/>
-        <property name="beanshell" value="${classext}/bsh-2.0b4.jar"/>
-        <property name="swinglayout" value="${classext}/swing-layout-1.0.4.jar"/>
-        <property name="commonsmath" value="${classext}/commons-math-2.0.jar"/>
-        <property name="swingx" value="${classext}/swingx-0.9.5.jar"/>
-
-	<path id="project.MMPlugins.path">
-		<pathelement location="${MMPluginDir}"/>
-	</path>
-
-	<path id="project.class.path">
-		<pathelement location="${MMCoreJ}" />
-		<pathelement location="${MMPluginDir}/MMJ_.jar"/>
-
-		<pathelement location="${IJ}" />
-		<pathelement location="${beanshell}" />
-		<pathelement location="${swinglayout}" />
-		<pathelement location="${commonsmath}" />
-		<pathelement location="${swingx}" />
-
-	</path>
-
-	<target name="compile" description="Compile Tracker plugin.">
-		<mkdir dir="build" />
-		<javac srcdir="./src" destdir="./build" optimize="on" source="1.5" target="1.5" debug="on">
-			<classpath refid="project.class.path" />
-		</javac>
-		<copy todir="./build/">
-			<fileset dir="./src/" includes="**/*.form" />
-		</copy>
-	</target>
-
-	<target name="build" description="Build Tracker.jar">
-		<jar jarfile="Tracker.jar" basedir="build" />
-		<copy file="Tracker.jar" todir="${MMPluginsDir-inst}" />
-	</target>
-	
-	<target name="clean" description="Delete the Tracker build files.">
-		<delete dir="build" />
-		<delete file="Tracker.jar" />
-	</target>
-	
-</project>
diff --git a/plugins/TwoPhoton/build.xml b/plugins/TwoPhoton/build.xml
new file mode 100644
index 0000000000..d83273a739
--- /dev/null
+++ b/plugins/TwoPhoton/build.xml
@@ -0,0 +1,3 @@
+<project name="TwoPhoton" default="jar">
+	<import file="../javapluginbuild.xml"/>
+</project>
diff --git a/plugins/build.xml b/plugins/build.xml
new file mode 100644
index 0000000000..2ef1270a21
--- /dev/null
+++ b/plugins/build.xml
@@ -0,0 +1,34 @@
+<project name="mm.plugins" basedir="." default="jar">
+	<macrodef name="run-all">
+		<attribute name="target"/>
+		<sequential>
+			<subant target="@{target}">
+				<fileset dir="." includes="*/build.xml"/>
+			</subant>
+		</sequential>
+	</macrodef>
+
+	<target name="prerequisites">
+		<run-all target="prerequisites"/>
+	</target>
+
+	<target name="compile">
+		<run-all target="compile"/>
+	</target>
+
+	<target name="copy-files">
+		<run-all target="copy-files"/>
+	</target>
+
+	<target name="jar">
+		<run-all target="jar"/>
+	</target>
+
+	<target name="install">
+		<run-all target="install"/>
+	</target>
+
+	<target name="clean">
+		<run-all target="clean"/>
+	</target>
+</project>
diff --git a/plugins/clojurepluginbuild.xml b/plugins/clojurepluginbuild.xml
new file mode 100644
index 0000000000..edab0d7a36
--- /dev/null
+++ b/plugins/clojurepluginbuild.xml
@@ -0,0 +1,8 @@
+<project name="mm.clojurepluginbuild">
+	<!-- This file is intended to be used via 'import' in each plugin
+	     project's buildfile -->
+
+	<include file="pluginprops.xml"/>
+	<import file="../buildscripts/clojurebuild.xml"/>
+	<include file="pluginpaths.xml"/>
+</project>
diff --git a/plugins/javapluginbuild.xml b/plugins/javapluginbuild.xml
new file mode 100644
index 0000000000..b3bc7f8769
--- /dev/null
+++ b/plugins/javapluginbuild.xml
@@ -0,0 +1,8 @@
+<project name="mm.javapluginbuild">
+	<!-- This file is intended to be used via 'import' in each plugin
+	     project's buildfile -->
+
+	<include file="pluginprops.xml"/>
+	<import file="../buildscripts/javabuild.xml"/>
+	<include file="pluginpaths.xml"/>
+</project>
diff --git a/plugins/pluginpaths.xml b/plugins/pluginpaths.xml
new file mode 100644
index 0000000000..39f8680af0
--- /dev/null
+++ b/plugins/pluginpaths.xml
@@ -0,0 +1,6 @@
+<project name="mm.pluginpaths">
+	<path id="project.classpath">
+		<path refid="mm.java.plugin.defaultclasspath"/>
+		<path refid="plugin.classpath"/>
+	</path>
+</project>
diff --git a/plugins/pluginprops.xml b/plugins/pluginprops.xml
new file mode 100644
index 0000000000..e32dc1cf29
--- /dev/null
+++ b/plugins/pluginprops.xml
@@ -0,0 +1,11 @@
+<project name="mm.pluginprops">
+	<include file="../buildscripts/buildprops.xml"/>
+
+	<property name="product" value="${ant.project.name}"/>
+	<property name="intdir" location="${mm.java.plugin.intdir}/${product}"/>
+	<property name="outdir" location="${mm.java.plugin.outdir}"/>
+	<property name="installdir" location="${mm.java.plugin.installdir}"/>
+
+	<!-- Additional classpath items for plugin; empty by default -->
+	<path id="plugin.classpath"/>
+</project>