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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/artemis">Debian Med / artemis</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/artemis/commit/94bbfb9b31ffb3b4efab31592a0872cccd162f09">94bbfb9b</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-01-28T20:27:40Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add *.poms file
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/artemis/commit/5095bdfdc3ba21a8208802814b979144d3c9319a">5095bdfd</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-01-29T08:20:36Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge output of mh_make
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/artemis/commit/4e6cac630f81492e93d421e87daf9847cce3818a">4e6cac63</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-01-29T08:35:26Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Remove unknown patches which are better dealt with debian/maven.ignore
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/artemis/commit/9844ab13216e1fbcac6d75f913094fdd79835e86">9844ab13</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-01-29T08:36:05Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix icon conversion
</pre>
</li>
</ul>
<h4>11 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#92000686a8bfcf22560c8fe819eeee2030f576e9">
debian/artemis.install
</a>
</li>
<li class="file-stats">
<a href="#85846adac02c5c84ad34148f42c842761d6be3cf">
<span class="new-file">
+
debian/artemis.poms
</span>
</a>
</li>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
</a>
</li>
<li class="file-stats">
<a href="#5f7c96eb17e78b0de55008d54b51e8dee2f412bc">
<span class="new-file">
+
debian/maven.cleanIgnoreRules
</span>
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</li>
<li class="file-stats">
<a href="#26121dc92cd4cd9822d2e9e2b619b799bf9a51f4">
debian/maven.ignoreRules
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</li>
<li class="file-stats">
<a href="#d006b76813d91cccc2a85e222d10982eb5d52728">
<span class="new-file">
+
debian/maven.properties
</span>
</a>
</li>
<li class="file-stats">
<a href="#24b90c28b48ee27d2ecad460d66ac6959df5c033">
<span class="new-file">
+
debian/maven.publishedRules
</span>
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</li>
<li class="file-stats">
<a href="#58530b38acb0fa3a65612c676abaea46c4a3f2f3">
<span class="new-file">
+
debian/maven.rules
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</a>
</li>
<li class="file-stats">
<a href="#c5ee830446e798a8c0ef00f7cc365fda858d547a">
<span class="deleted-file">
−
debian/patches/maven_depencencies.patch
</span>
</a>
</li>
<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
</a>
</li>
<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="92000686a8bfcf22560c8fe819eeee2030f576e9">
<a href="https://salsa.debian.org/med-team/artemis/compare/edcab6c5dc8765627b10bd34f4e892dea2653511...9844ab13216e1fbcac6d75f913094fdd79835e86#92000686a8bfcf22560c8fe819eeee2030f576e9"><strong>debian/artemis.install</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -3,4 +3,3 @@ jar_build/act.jar usr/share/java/</td>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="php"><span class="nx">jar_build</span><span class="o" style="font-weight: 600;">/</span><span class="nx">bamview</span><span class="o" style="font-weight: 600;">.</span><span class="nx">jar</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">share</span><span class="o" style="font-weight: 600;">/</span><span class="nx">java</span><span class="o" style="font-weight: 600;">/</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="php"><span class="nx">jar_build</span><span class="o" style="font-weight: 600;">/</span><span class="nx">dnaplotter</span><span class="o" style="font-weight: 600;">.</span><span class="nx">jar</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">share</span><span class="o" style="font-weight: 600;">/</span><span class="nx">java</span><span class="o" style="font-weight: 600;">/</span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="php"><span class="nx">debian</span><span class="o" style="font-weight: 600;">/</span><span class="nx">desktop</span><span class="o" style="font-weight: 600;">/*.</span><span class="nx">desktop</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">share</span><span class="o" style="font-weight: 600;">/</span><span class="nx">applications</span><span class="o" style="font-weight: 600;">/</span></span></pre>
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<td class="diff-line-num old old_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="php"><span class="nx">images</span><span class="o" style="font-weight: 600;">/</span><span class="nx">helix</span><span class="o" style="font-weight: 600;">.</span><span class="nx">png</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">share</span><span class="o" style="font-weight: 600;">/</span><span class="nx">icons</span><span class="o" style="font-weight: 600;">/</span><span class="nx">hicolor</span><span class="o" style="font-weight: 600;">/</span><span class="mi" style="color: #099;">96</span><span class="nx">x96</span><span class="o" style="font-weight: 600;">/</span><span class="nx">apps</span><span class="o" style="font-weight: 600;">/</span></span></pre>
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<li id="85846adac02c5c84ad34148f42c842761d6be3cf">
<a href="https://salsa.debian.org/med-team/artemis/compare/edcab6c5dc8765627b10bd34f4e892dea2653511...9844ab13216e1fbcac6d75f913094fdd79835e86#85846adac02c5c84ad34148f42c842761d6be3cf"><strong>debian/artemis.poms</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext"># List of POM files for the package</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"># Format of this file is:</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"># <path to pom file> [option]*</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"># where option can be:</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"># --ignore: ignore this POM and its artifact if any</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"># --ignore-pom: don't install the POM. To use on POM files that are created</span>
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<td class="diff-line-num new new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"># temporarily for certain artifacts such as Javadoc jars. [mh_install, mh_installpoms]</span>
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<td class="diff-line-num new new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"># --no-parent: remove the <parent> tag from the POM</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"># --package=<package>: an alternative package to use when installing this POM</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"># and its artifact</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"># --has-package-version: to indicate that the original version of the POM is the same as the upstream part</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"># of the version for the package.</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"># --keep-elements=<elem1,elem2>: a list of XML elements to keep in the POM</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"># during a clean operation with mh_cleanpom or mh_installpom</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"># --artifact=<path>: path to the build artifact associated with this POM,</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"># it will be installed when using the command mh_install. [mh_install]</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"># --java-lib: install the jar into /usr/share/java to comply with Debian</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"># packaging guidelines</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext"># --usj-name=<name>: name to use when installing the library in /usr/share/java</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"># --usj-version=<version>: version to use when installing the library in /usr/share/java</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext"># --no-usj-versionless: don't install the versionless link in /usr/share/java</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext"># --dest-jar=<path>: the destination for the real jar.</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext"># It will be installed with mh_install. [mh_install]</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext"># --classifier=<classifier>: Optional, the classifier for the jar. Empty by default.</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext"># --site-xml=<location>: Optional, the location for site.xml if it needs to be installed.</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext"># Empty by default. [mh_install]</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">#</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext">pom.xml --has-package-version</span></pre>
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<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/artemis/compare/edcab6c5dc8765627b10bd34f4e892dea2653511...9844ab13216e1fbcac6d75f913094fdd79835e86#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -4,37 +4,32 @@ Uploaders: Afif Elghraoui <afif@debian.org></td>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">Section: science</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">Priority: optional</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">Build-Depends: debhelper (>= 12~),</span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext"> default-jdk-headless,</span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext"> javahelper,</span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext"> maven-debian-helper,</span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext"> libmaven-enforcer-plugin-java,</span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext"> libmaven-install-plugin-java,</span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext"> libproperties-maven-plugin-java,</span>
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13
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="plaintext"> libmaven-antrun-plugin-java,</span>
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14
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="plaintext"> libmaven-resources-plugin-java,</span>
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15
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="plaintext"> libbuild-helper-maven-plugin-java,</span>
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16
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="plaintext"> libmaven-jar-plugin-java,</span>
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17
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="plaintext"> libmaven-shade-plugin-java,</span>
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18
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="plaintext"> libmaven-assembly-plugin-java,</span>
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19
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="plaintext"> libbiojava-java,</span>
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20
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="plaintext"> libj2ssh-java,</span>
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21
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="plaintext"> libibatis-java,</span>
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22
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="plaintext"> liblog4j1.2-java,</span>
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23
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="plaintext"> libpostgresql-jdbc-java,</span>
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24
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="plaintext"> picard-tools,</span>
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25
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="plaintext"> libhtsjdk-java,</span>
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26
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="plaintext"> libcommons-net-java,</span>
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27
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="plaintext"> libcommons-lang3-java,</span>
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28
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="plaintext"> libbatik-java,</span>
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29
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="plaintext"> jemboss,</span>
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30
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="plaintext"># For tests</span>
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31
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="plaintext"> ant,</span>
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32
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="plaintext"> ant-optional,</span>
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33
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="plaintext"> junit4,</span>
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<td class="diff-line-num old old_line" data-linenumber="34" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
34
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="plaintext"> libhamcrest-java,</span>
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35
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="plaintext"> libjs-jquery,</span>
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<td class="diff-line-num old old_line" data-linenumber="36" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
36
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="plaintext"># To convert gifs to png because gif is not a supported icon format</span>
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<td class="diff-line-num old old_line" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
37
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="plaintext"> imagemagick</span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> default-jdk,</span>
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<td class="diff-line-num new new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> maven-debian-helper (>= 2.1)</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">Build-Depends-Indep: junit4 (>= 4.12),</span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> libbatik-java (>= 1.10),</span>
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<td class="diff-line-num new new_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> libcommons-lang3-java,</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> libcommons-logging-java (>= 1.2),</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> libcommons-net-java (>= 3.6),</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"> liblog4j1.2-java (>= 1.2.17),</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"> libmaven-antrun-plugin-java (>= 1.8),</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"> libmaven-install-plugin-java (>= 2.5.2),</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"> libmaven-shade-plugin-java (>= 3.1.1),</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"> libpostgresql-jdbc-java (>= 42.2.5),</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext"> libslf4j-java (>= 1.7.25),</span>
</pre>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"> libmaven-enforcer-plugin-java,</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext"> libmaven-resources-plugin-java,</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext"> libbuild-helper-maven-plugin-java,</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext"> libmaven-jar-plugin-java,</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext"> libmaven-shade-plugin-java,</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext"> libmaven-assembly-plugin-java,</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext"> libbiojava-java,</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext"> libj2ssh-java,</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext"> libibatis-java,</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext"> picard-tools,</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext"> libhtsjdk-java,</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext"> jemboss,</span>
</pre>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext"> imagemagick</span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="plaintext">Standards-Version: 4.3.0</span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/artemis</span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/artemis.git</span>
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<a href="https://salsa.debian.org/med-team/artemis/compare/edcab6c5dc8765627b10bd34f4e892dea2653511...9844ab13216e1fbcac6d75f913094fdd79835e86#5f7c96eb17e78b0de55008d54b51e8dee2f412bc"><strong>debian/maven.cleanIgnoreRules</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext"></span></pre>
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<a href="https://salsa.debian.org/med-team/artemis/compare/edcab6c5dc8765627b10bd34f4e892dea2653511...9844ab13216e1fbcac6d75f913094fdd79835e86#26121dc92cd4cd9822d2e9e2b619b799bf9a51f4"><strong>debian/maven.ignoreRules</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext"># see https://lists.debian.org/debian-java/2019/01/msg00063.html</span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">org.jacoco jacoco-maven-plugin</span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext">org.apache.maven.plugins maven-enforcer-plugin</span></pre>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">cglib cglib-nodep * * * *</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">org.apache.maven.plugins maven-jarsigner-plugin * * * *</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">org.apache.maven.plugins maven-javadoc-plugin * * * *</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">org.codehaus.mojo properties-maven-plugin * * * *</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">org.evosuite evosuite-standalone-runtime * * * *</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">org.jacoco jacoco-maven-plugin * * * *</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">org.mockito mockito-core * * * *</span></pre>
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<a href="https://salsa.debian.org/med-team/artemis/compare/edcab6c5dc8765627b10bd34f4e892dea2653511...9844ab13216e1fbcac6d75f913094fdd79835e86#d006b76813d91cccc2a85e222d10982eb5d52728"><strong>debian/maven.properties</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="properties"><span class="c" style="color: #998; font-style: italic;"># Include here properties to pass to Maven during the build.</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="properties"><span class="c" style="color: #998; font-style: italic;"># For example:</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="properties"><span class="c" style="color: #998; font-style: italic;"># maven.test.skip=true</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="properties"><span class="c" style="color: #998; font-style: italic;"># project.build.sourceEncoding=UTF-8</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="properties"></span></pre>
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<a href="https://salsa.debian.org/med-team/artemis/compare/edcab6c5dc8765627b10bd34f4e892dea2653511...9844ab13216e1fbcac6d75f913094fdd79835e86#24b90c28b48ee27d2ecad460d66ac6959df5c033"><strong>debian/maven.publishedRules</strong></a>
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<a href="https://salsa.debian.org/med-team/artemis/compare/edcab6c5dc8765627b10bd34f4e892dea2653511...9844ab13216e1fbcac6d75f913094fdd79835e86#58530b38acb0fa3a65612c676abaea46c4a3f2f3"><strong>debian/maven.rules</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">junit junit jar s/4\..*/4.x/ * *</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">uk.ac.sanger artemis jar s/.*/debian/ * *</span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">commons-logging s/commons-logging-api/commons-logging/ * s/.*/debian/ * *</span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">log4j log4j * s/1\.2\..*/1.2.x/ * *</span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">org.apache.maven.plugins maven-enforcer-plugin * s/.*/debian/ * *</span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">org.apache.rat apache-rat-plugin * s/.*/debian/ * *</span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">org.codehaus.plexus plexus-container-default * * * *</span></pre>
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<li id="c5ee830446e798a8c0ef00f7cc365fda858d547a">
<a href="https://salsa.debian.org/med-team/artemis/compare/edcab6c5dc8765627b10bd34f4e892dea2653511...9844ab13216e1fbcac6d75f913094fdd79835e86#c5ee830446e798a8c0ef00f7cc365fda858d547a"><strong>debian/patches/maven_depencencies.patch</strong>
deleted
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1
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/pom.xml</span></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/pom.xml</span></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -360,7 +360,6 @@ Artemis is written in Java, and is avail</span></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="diff"> <inherited>true</inherited></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="diff"> <groupId>org.apache.maven.plugins</groupId></span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="diff"> <artifactId>maven-enforcer-plugin</artifactId></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- <version>1.3.1</version></span></span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="diff"> <executions></span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="diff"> <execution></span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="diff"> <id>enforce-maven-3</id></span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -499,7 +498,6 @@ Artemis is written in Java, and is avail</span></span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="diff"> <plugin></span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="diff"> <groupId>org.apache.maven.plugins</groupId></span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="diff"> <artifactId>maven-resources-plugin</artifactId></span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- <version>3.0.2</version></span></span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="diff"> <executions></span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="diff"> <!-- Copy etc on to classpath --></span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="diff"> <execution></span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -554,7 +552,6 @@ Artemis is written in Java, and is avail</span></span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="diff"> <plugin></span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="diff"> <groupId>org.apache.maven.plugins</groupId></span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="diff"> <artifactId>maven-jar-plugin</artifactId></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- <version>3.1.0</version></span></span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="diff"> <configuration></span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="diff"> <archive></span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="diff"> <manifest></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -616,55 +613,12 @@ Artemis is written in Java, and is avail</span></span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="diff"> </configuration></span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="diff"> </plugin></span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- <!-- =================================== Run Jacoco coverage report ======================================--></span></span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- </span></span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- <plugin></span></span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- <groupId>org.jacoco</groupId></span></span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- <artifactId>jacoco-maven-plugin</artifactId></span></span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- <version>0.8.2</version></span></span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- <configuration></span></span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- <skip>${skip.coverage.reporting}</skip></span></span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- </configuration></span></span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- <executions></span></span>
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- <execution></span></span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- <id>pre-unit-test</id></span></span>
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- <goals></span></span>
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- <goal>prepare-agent</goal></span></span>
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- </goals></span></span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- <configuration></span></span>
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- <output>file</output></span></span>
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- <!-- Sets the path to the file which contains the execution data. --></span></span>
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- <destFile>${project.build.directory}/jacoco-ut.exec</destFile></span></span>
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- <!-- Sets the name of the property containing the settings for JaCoCo </span></span>
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- runtime agent. --></span></span>
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- <propertyName>surefireArgLine</propertyName></span></span>
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- </configuration></span></span>
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<pre style="margin: 0;">-<span id="LC54" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- </execution></span></span>
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<pre style="margin: 0;">-<span id="LC55" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- <!-- Ensures that the code coverage report for unit tests is created after </span></span>
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<pre style="margin: 0;">-<span id="LC56" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- unit tests have been run. --></span></span>
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<pre style="margin: 0;">-<span id="LC57" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- <execution></span></span>
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<pre style="margin: 0;">-<span id="LC58" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- <id>post-unit-test</id></span></span>
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<pre style="margin: 0;">-<span id="LC59" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- <phase>test</phase></span></span>
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<pre style="margin: 0;">-<span id="LC60" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- <goals></span></span>
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<pre style="margin: 0;">-<span id="LC61" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- <goal>report</goal></span></span>
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<pre style="margin: 0;">-<span id="LC62" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- </goals></span></span>
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<pre style="margin: 0;">-<span id="LC63" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- <configuration></span></span>
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<pre style="margin: 0;">-<span id="LC64" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- <dataFile>${project.build.directory}/jacoco-ut.exec</dataFile></span></span>
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<pre style="margin: 0;">-<span id="LC65" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- <outputDirectory>${project.build.directory}/coverage-report</outputDirectory></span></span>
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<pre style="margin: 0;">-<span id="LC66" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- <excludes></span></span>
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<pre style="margin: 0;">-<span id="LC67" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- <exclude>org/**</exclude></span></span>
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<pre style="margin: 0;">-<span id="LC68" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- </excludes></span></span>
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<pre style="margin: 0;">-<span id="LC69" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- </configuration></span></span>
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<pre style="margin: 0;">-<span id="LC70" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- </execution></span></span>
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<pre style="margin: 0;">-<span id="LC71" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- </executions></span></span>
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<pre style="margin: 0;">-<span id="LC72" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- </plugin></span></span>
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<pre style="margin: 0;">-<span id="LC73" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC74" class="line" lang="diff"> <!-- ============= Package the code and dependent jars into one executable jar for each applications ========= --></span>
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<pre style="margin: 0;">-<span id="LC75" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC76" class="line" lang="diff"> <plugin></span>
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<pre style="margin: 0;">-<span id="LC77" class="line" lang="diff"> <groupId>org.apache.maven.plugins</groupId></span>
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<pre style="margin: 0;">-<span id="LC78" class="line" lang="diff"> <artifactId>maven-shade-plugin</artifactId></span>
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79
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<pre style="margin: 0;">-<span id="LC79" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- <version>3.1.0</version></span></span>
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<pre style="margin: 0;">-<span id="LC80" class="line" lang="diff"> <executions></span>
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<pre style="margin: 0;">-<span id="LC81" class="line" lang="diff"> <execution></span>
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<pre style="margin: 0;">-<span id="LC82" class="line" lang="diff"> <id>package-win-artemis-jar</id></span>
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<pre style="margin: 0;">-<span id="LC83" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1005,66 +959,12 @@ Artemis is written in Java, and is avail</span></span>
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<pre style="margin: 0;">-<span id="LC84" class="line" lang="diff"> </plugin></span>
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<pre style="margin: 0;">-<span id="LC85" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC86" class="line" lang="diff"> </span>
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87
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<pre style="margin: 0;">-<span id="LC87" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- <!-- ============================= Sign executable jar files ============================ --></span></span>
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88
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<pre style="margin: 0;">-<span id="LC88" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- </span></span>
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<pre style="margin: 0;">-<span id="LC89" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- <plugin></span></span>
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<pre style="margin: 0;">-<span id="LC90" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- <groupId>org.apache.maven.plugins</groupId></span></span>
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91
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<pre style="margin: 0;">-<span id="LC91" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- <artifactId>maven-jarsigner-plugin</artifactId></span></span>
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92
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<pre style="margin: 0;">-<span id="LC92" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- <version>1.4</version></span></span>
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<pre style="margin: 0;">-<span id="LC93" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- <executions></span></span>
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<pre style="margin: 0;">-<span id="LC94" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- <execution></span></span>
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<pre style="margin: 0;">-<span id="LC95" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- <id>sign-win-jars</id></span></span>
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<pre style="margin: 0;">-<span id="LC96" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- <phase>package</phase></span></span>
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<pre style="margin: 0;">-<span id="LC97" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- <goals></span></span>
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98
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<pre style="margin: 0;">-<span id="LC98" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- <goal>sign</goal></span></span>
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99
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<pre style="margin: 0;">-<span id="LC99" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- </goals></span></span>
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100
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<pre style="margin: 0;">-<span id="LC100" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- <configuration></span></span>
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<td class="diff-line-num old old_line" data-linenumber="101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
101
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<pre style="margin: 0;">-<span id="LC101" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- <skip>${jarsigner.skip}</skip></span></span>
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102
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<pre style="margin: 0;">-<span id="LC102" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- <verbose>false</verbose></span></span>
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<td class="diff-line-num old old_line" data-linenumber="103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
103
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<pre style="margin: 0;">-<span id="LC103" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- <processMainArtifact>false</processMainArtifact></span></span>
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<td class="diff-line-num old old_line" data-linenumber="104" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
104
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<pre style="margin: 0;">-<span id="LC104" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- <processAttachedArtifacts>false</processAttachedArtifacts></span></span>
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<td class="diff-line-num old old_line" data-linenumber="105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
105
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<pre style="margin: 0;">-<span id="LC105" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- <archiveDirectory>target/win-jars</archiveDirectory></span></span>
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<td class="diff-line-num old old_line" data-linenumber="106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
106
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<pre style="margin: 0;">-<span id="LC106" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- <keystore>${signer-keystore-path}</keystore></span></span>
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<td class="diff-line-num old old_line" data-linenumber="107" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
107
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<pre style="margin: 0;">-<span id="LC107" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- <storetype>${signer-keystore-type}</storetype></span></span>
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<td class="diff-line-num old old_line" data-linenumber="108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
108
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<pre style="margin: 0;">-<span id="LC108" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- <alias>${signer-keystore-alias}</alias></span></span>
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<td class="diff-line-num old old_line" data-linenumber="109" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
109
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<pre style="margin: 0;">-<span id="LC109" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- <storepass>${signer-keystore-password}</storepass></span></span>
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<td class="diff-line-num old old_line" data-linenumber="110" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
110
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<pre style="margin: 0;">-<span id="LC110" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- <keypass>${signer-keystore-password}</keypass></span></span>
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<td class="diff-line-num old old_line" data-linenumber="111" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
111
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<pre style="margin: 0;">-<span id="LC111" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- <removeExistingSignatures>true</removeExistingSignatures></span></span>
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<td class="diff-line-num old old_line" data-linenumber="112" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
112
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<pre style="margin: 0;">-<span id="LC112" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- <tsa>http://timestamp.comodoca.com/rfc3161</tsa></span></span>
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<td class="diff-line-num old old_line" data-linenumber="113" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
113
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<pre style="margin: 0;">-<span id="LC113" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- </configuration></span></span>
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114
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<pre style="margin: 0;">-<span id="LC114" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- </execution></span></span>
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115
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<pre style="margin: 0;">-<span id="LC115" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- <execution></span></span>
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<td class="diff-line-num old old_line" data-linenumber="116" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
116
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<pre style="margin: 0;">-<span id="LC116" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- <id>sign-default-jars</id></span></span>
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<td class="diff-line-num old old_line" data-linenumber="117" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
117
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<pre style="margin: 0;">-<span id="LC117" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- <phase>package</phase></span></span>
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118
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<pre style="margin: 0;">-<span id="LC118" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- <goals></span></span>
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119
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<pre style="margin: 0;">-<span id="LC119" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- <goal>sign</goal></span></span>
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120
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<pre style="margin: 0;">-<span id="LC120" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- </goals></span></span>
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121
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<pre style="margin: 0;">-<span id="LC121" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- <configuration></span></span>
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122
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<pre style="margin: 0;">-<span id="LC122" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- <skip>${jarsigner.skip}</skip></span></span>
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123
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<pre style="margin: 0;">-<span id="LC123" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- <verbose>false</verbose></span></span>
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124
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<pre style="margin: 0;">-<span id="LC124" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- <processMainArtifact>false</processMainArtifact></span></span>
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125
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<pre style="margin: 0;">-<span id="LC125" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- <processAttachedArtifacts>false</processAttachedArtifacts></span></span>
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126
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<pre style="margin: 0;">-<span id="LC126" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- <archiveDirectory>target/jars</archiveDirectory></span></span>
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127
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<pre style="margin: 0;">-<span id="LC127" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- <keystore>${signer-keystore-path}</keystore></span></span>
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<td class="diff-line-num old old_line" data-linenumber="128" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
128
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<pre style="margin: 0;">-<span id="LC128" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- <storetype>${signer-keystore-type}</storetype></span></span>
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129
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<pre style="margin: 0;">-<span id="LC129" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- <alias>${signer-keystore-alias}</alias></span></span>
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130
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<pre style="margin: 0;">-<span id="LC130" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- <storepass>${signer-keystore-password}</storepass></span></span>
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131
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<pre style="margin: 0;">-<span id="LC131" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- <keypass>${signer-keystore-password}</keypass></span></span>
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132
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<pre style="margin: 0;">-<span id="LC132" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- <removeExistingSignatures>true</removeExistingSignatures></span></span>
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133
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<pre style="margin: 0;">-<span id="LC133" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- <tsa>http://timestamp.comodoca.com/rfc3161</tsa></span></span>
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134
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<pre style="margin: 0;">-<span id="LC134" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- </configuration></span></span>
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135
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<pre style="margin: 0;">-<span id="LC135" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- </execution></span></span>
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136
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<pre style="margin: 0;">-<span id="LC136" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- </executions></span></span>
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137
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<pre style="margin: 0;">-<span id="LC137" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- </span></span>
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138
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<pre style="margin: 0;">-<span id="LC138" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- </plugin></span></span>
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139
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<pre style="margin: 0;">-<span id="LC139" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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140
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<pre style="margin: 0;">-<span id="LC140" class="line" lang="diff"> </span>
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141
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<pre style="margin: 0;">-<span id="LC141" class="line" lang="diff"> <!-- ========================== Create release zips ============================ --></span>
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142
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<pre style="margin: 0;">-<span id="LC142" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC143" class="line" lang="diff"> <plugin></span>
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<pre style="margin: 0;">-<span id="LC144" class="line" lang="diff"> <groupId>org.apache.maven.plugins</groupId></span>
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<pre style="margin: 0;">-<span id="LC145" class="line" lang="diff"> <artifactId>maven-assembly-plugin</artifactId></span>
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<pre style="margin: 0;">-<span id="LC146" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- <version>3.1.0</version></span></span>
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<pre style="margin: 0;">-<span id="LC147" class="line" lang="diff"> <executions></span>
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<pre style="margin: 0;">-<span id="LC148" class="line" lang="diff"> <execution></span>
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<pre style="margin: 0;">-<span id="LC149" class="line" lang="diff"> <id>create-unix-release</id></span>
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<pre style="margin: 0;">-<span id="LC150" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1350,10 +1250,6 @@ Artemis is written in Java, and is avail</span></span>
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<pre style="margin: 0;">-<span id="LC151" class="line" lang="diff"> <properties></span>
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<pre style="margin: 0;">-<span id="LC152" class="line" lang="diff"> <skip.tests>false</skip.tests></span>
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<pre style="margin: 0;">-<span id="LC153" class="line" lang="diff"> <evosuite.exclude.filter></evosuite.exclude.filter></span>
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<pre style="margin: 0;">-<span id="LC154" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- <jarsigner.skip>false</jarsigner.skip></span></span>
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<pre style="margin: 0;">-<span id="LC155" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- <skip.artifact.creation>false</skip.artifact.creation></span></span>
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<pre style="margin: 0;">-<span id="LC156" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- <skip.coverage.reporting>false</skip.coverage.reporting></span></span>
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<pre style="margin: 0;">-<span id="LC157" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- <skip.javadoc>false</skip.javadoc></span></span>
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<pre style="margin: 0;">-<span id="LC158" class="line" lang="diff"> </span>
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159
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<pre style="margin: 0;">-<span id="LC159" class="line" lang="diff"> <build.profile.id>release</build.profile.id></span>
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160
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<pre style="margin: 0;">-<span id="LC160" class="line" lang="diff"> </properties> </span></pre>
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<a href="https://salsa.debian.org/med-team/artemis/compare/edcab6c5dc8765627b10bd34f4e892dea2653511...9844ab13216e1fbcac6d75f913094fdd79835e86#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2,4 +2,3 @@ samreader.patch</td>
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2
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">use-lang3.patch</span>
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3
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">#build-test.patch</span>
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4
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">#disable-tests.patch</span></pre>
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5
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext">maven_depencencies.patch</span></pre>
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<a href="https://salsa.debian.org/med-team/artemis/compare/edcab6c5dc8765627b10bd34f4e892dea2653511...9844ab13216e1fbcac6d75f913094fdd79835e86#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -35,13 +35,17 @@ CLASSPATH += /usr/share/EMBOSS/jemboss/lib/jemboss.jar \</td>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="plaintext">export CLASSPATH := $(subst $(space),:,$(strip $(CLASSPATH)))</span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="plaintext">%:</span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="plaintext"> dh $@<span class="idiff left right"> --with javahelper --buildsystem=maven</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext"> dh $@</span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="plaintext">__override_dh_auto_build:</span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="plaintext"> dh_auto_build -- jar</span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="plaintext"> sed 's|@CLASSPATH@|$(subst :,$(space),$(subst $(CURDIR),/usr/share/java/artemis.jar,$(CLASSPATH)))|g' debian/artemis.manifest.in > \</span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="plaintext"> debian/artemis.manifest</span>
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="plaintext"> convert images/helix.gif -resize 96x96\! images/helix.png</span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext">override_dh_install:</span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext"> dh_install</span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext"> mkdir -p debian/$(DEB_SOURCE)/usr/share/icons/hicolor/96x96/apps/</span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext"> convert src/main/resources/images/helix.gif -resize 96x96\! debian/$(DEB_SOURCE)/usr/share/icons/hicolor/96x96/apps/helix.png</span>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="plaintext">__override_dh_auto_test:</span>
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="plaintext">ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))</span>
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