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Merge branch 'better-eclipse-behavior'
This branch attempts to make the codebase usable from Eclipse. It does not fully succeed; the unit tests still have problems. Fortunately, we will be ditching the SJC2-annotation-based plugins soon, which will hopefully make the remaining the Eclipse-related issues moot.
2 parents dd98459 + f178f00 commit 05a1e18

19 files changed

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‎imagej/imagej-ops2/pom.xml‎

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<?xml version="1.0" encoding="UTF-8"?>
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<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
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<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 https://maven.apache.org/maven-v4_0_0.xsd">
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<modelVersion>4.0.0</modelVersion>
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<parent>

‎imagej/imagej-ops2/src/main/java/module-info.java‎

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opens net.imagej.ops2.types.maxValue to org.scijava, org.scijava.ops.engine;
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opens net.imagej.ops2.types.minValue to org.scijava, org.scijava.ops.engine;
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requires java.desktop;
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requires java.xml; // TEMP: for org.scijava:scijava-common org.scijava.util.POM
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requires java.scripting;
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requires net.imagej;
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requires net.imagej.mesh;
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requires net.imglib2.roi;
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requires org.joml;
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requires org.scijava;
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requires org.scijava.function;
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requires org.scijava.ops.api;
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requires org.scijava.ops.engine;
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requires org.scijava.ops.spi;
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requires org.scijava.parsington;
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requires org.scijava.types;
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requires jama;
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requires imglib2.algorithm.fft;
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requires mines.jtk;
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requires org.scijava.function;
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requires org.scijava.ops.api;
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requires org.scijava.ops.spi;
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}

‎imagej/imagej-ops2/src/main/java/net/imagej/ops2/geom/geom2d/DefaultSizePolygon.java‎

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package net.imagej.ops2.geom.geom2d;
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import java.awt.geom.Area;
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import net.imglib2.RealLocalizable;
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import net.imglib2.roi.geom.real.Polygon2D;
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import net.imglib2.type.numeric.real.DoubleType;
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import org.scijava.plugin.Plugin;
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/**
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* Specific implementation of {@link Area} for a Polygon2D.
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* Computes the size (i.e. area) of a {@link Polygon2D}.
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*
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* @author Daniel Seebacher (University of Konstanz)
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*/

‎imagej/imagej-testutil/pom.xml‎

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<?xml version="1.0" encoding="UTF-8"?>
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<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
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<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 https://maven.apache.org/maven-v4_0_0.xsd">
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<modelVersion>4.0.0</modelVersion>
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<parent>

‎pom.xml‎

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<?xml version="1.0" encoding="UTF-8"?>
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<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
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<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 https://maven.apache.org/xsd/maven-4.0.0.xsd">
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<modelVersion>4.0.0</modelVersion>
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<parent>
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<groupId>org.scijava</groupId>
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<artifactId>pom-scijava</artifactId>
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<version>30.0.0</version>
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<version>31.1.0</version>
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<relativePath />
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</parent>
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<language>ruby</language>
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<script>
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# Append the source plugin annotations to the test plugin annotations
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require 'set'
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# Handle windows paths
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basedir = '${project.basedir}'.gsub /\\+/, '\\\\'
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sourceFile = basedir + '/target/classes/META-INF/json/org.scijava.plugin.Plugin'
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destFile = basedir + '/target/test-classes/META-INF/json/org.scijava.plugin.Plugin'
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File.open(sourceFile) do |input|
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data_to_copy = input.read()
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File.open(destFile, 'a') do |output|
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output.write(data_to_copy)
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end
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# Reads plugin metadata into a set of strings, one per plugin declaration.
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def read_plugins(path)
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delim = 'UNIQUE-SEQUENCE-THAT-NO-PLUGIN-WILL-EVER-USE'
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return File.exist?(path) ? File.read(path).sub('}{', '}' + delim + '{').split(delim).to_set : Set.new()
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end
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# Read in main and test scope plugin annotations.
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pluginsPath = 'META-INF/json/org.scijava.plugin.Plugin'
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mainPluginsPath = "#{basedir}/target/classes/#{pluginsPath}"
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testPluginsPath = "#{basedir}/target/test-classes/#{pluginsPath}"
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mainPlugins = read_plugins(mainPluginsPath)
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testPlugins = read_plugins(testPluginsPath)
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# Write out unioned plugin annotations to test scope plugin annotations.
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# Without this, the test scope code does not know of the main scope plugins.
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allPlugins = mainPlugins.union(testPlugins)
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unless allPlugins.empty?()
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require 'fileutils'
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FileUtils.mkdir_p File.dirname(testPluginsPath)
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File.write(testPluginsPath, allPlugins.to_a.join(''))
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end
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</script>
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</configuration>
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</plugins>
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</pluginManagement>
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</build>
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<profiles>
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<!--
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This profile lets Eclipse M2E work with the script-maven-plugin.
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-->
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<profile>
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<id>only-eclipse-incubator</id>
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<activation>
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<property>
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<name>m2e.version</name>
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</property>
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</activation>
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<build>
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<pluginManagement>
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<plugins>
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<plugin>
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<groupId>org.eclipse.m2e</groupId>
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<artifactId>lifecycle-mapping</artifactId>
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<version>1.0.0</version>
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<configuration>
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<lifecycleMappingMetadata>
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<pluginExecutions>
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<!--
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NB: Make Eclipse union the metadata indices on every build; see:
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https://www.eclipse.org/m2e/documentation/m2e-execution-not-covered.html
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-->
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<pluginExecution>
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<pluginExecutionFilter>
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<groupId>com.alexecollins.maven.plugin</groupId>
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<artifactId>script-maven-plugin</artifactId>
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<versionRange>${script-maven-plugin.version}</versionRange>
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<goals>
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<goal>execute</goal>
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</goals>
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</pluginExecutionFilter>
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<action>
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<execute>
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<runOnConfiguration>true</runOnConfiguration>
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<!--
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NB: You might think we could run the annotations
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union script once only, at configuration time.
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Unfortunately, when configuration happens in Eclipse,
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the plugin annotations have not yet been generated.
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So let's redo the union on every incremental build.
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That'll show 'em!
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-->
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<runOnIncremental>true</runOnIncremental>
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</execute>
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</action>
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</pluginExecution>
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</pluginExecutions>
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</lifecycleMappingMetadata>
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</configuration>
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</plugin>
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</plugins>
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</pluginManagement>
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</build>
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</profile>
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</profiles>
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</project>

‎scijava/scijava-discovery/pom.xml‎

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<?xml version="1.0" encoding="UTF-8"?>
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<project xmlns="http://maven.apache.org/POM/4.0.0"
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xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
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xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
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<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 https://maven.apache.org/xsd/maven-4.0.0.xsd">
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<modelVersion>4.0.0</modelVersion>
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<parent>

‎scijava/scijava-function/pom.xml‎

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<?xml version="1.0" encoding="UTF-8"?>
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<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
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<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 https://maven.apache.org/xsd/maven-4.0.0.xsd">
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<modelVersion>4.0.0</modelVersion>
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<parent>

‎scijava/scijava-ops-api/pom.xml‎

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<?xml version="1.0" encoding="UTF-8"?>
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<project xmlns="http://maven.apache.org/POM/4.0.0"
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xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
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xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
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<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 https://maven.apache.org/xsd/maven-4.0.0.xsd">
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<modelVersion>4.0.0</modelVersion>
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<parent>

‎scijava/scijava-ops-discovery/.gitignore‎

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This file was deleted.

‎scijava/scijava-ops-engine/pom.xml‎

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<?xml version="1.0" encoding="UTF-8"?>
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<project xmlns="http://maven.apache.org/POM/4.0.0"
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xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
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xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
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<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 https://maven.apache.org/xsd/maven-4.0.0.xsd">
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<modelVersion>4.0.0</modelVersion>
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<parent>

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