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<h3>
Pierre Gruet pushed to branch master
at <a href="https://salsa.debian.org/med-team/beast2-mcmc">Debian Med / beast2-mcmc</a>
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<h4>
Commits:
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<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/beast2-mcmc/-/commit/fa097ddeb3b8dc23fa5a6cc571a9f47dba0036de">fa097dde</a></strong>
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<span>by Pierre Gruet</span>
<i>at 2020-09-15T10:50:02+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Removing jsign from the build as it is needed for Microsoft Windows
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<strong><a href="https://salsa.debian.org/med-team/beast2-mcmc/-/commit/d59e3317d2ccccb9baf76d6b220d48f9fb7a52aa">d59e3317</a></strong>
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<span>by Pierre Gruet</span>
<i>at 2020-09-15T10:50:51+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Deleting accents in MCMC.java as they caused build failures
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<strong><a href="https://salsa.debian.org/med-team/beast2-mcmc/-/commit/5563694f37e510a88cd1af59e7f74c548b4983eb">5563694f</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2020-09-15T10:51:51+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Removing the import of useless and unpackaged org.fest.swing.security
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<h4>4 changed files:</h4>
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<li class="file-stats">
<a href="#c70c8de80400249838a0c9446a3f92115a86948c">
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+
debian/patches/accents_in_source.patch
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<a href="#48145ea6d5b9e8f96496083c8fc5a2df8a675d89">
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+
debian/patches/remove_import_swing_security.patch
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<a href="#eb03b62356d7a87ac94d69bcbedc01343e93f8a1">
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+
debian/patches/remove_jsign_from_build.patch
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<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
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<h4>Changes:</h4>
<li id="c70c8de80400249838a0c9446a3f92115a86948c">
<a href="https://salsa.debian.org/med-team/beast2-mcmc/-/compare/98151f7c6e58952310a65305316015b227ca4962...5563694f37e510a88cd1af59e7f74c548b4983eb#c70c8de80400249838a0c9446a3f92115a86948c"><strong>debian/patches/accents_in_source.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Description: Removing accents on names in a Java annotation</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"> Those accents caused build failures as javac tried to encode US-ASCII but</span>
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<td class="diff-line-num new new_line" data-linenumber="3" 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="LC3" class="line" lang="diff"> could not.</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="p">Author: Pierre Gruet <pgtdebian@free.fr></span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="p">Forwarded: not-needed</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"><span class="p">Last-Update: 2020-09-15</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff">--- a/src/beast/core/MCMC.java</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/beast/core/MCMC.java</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"><span class="p">@@ -49,9 +49,9 @@</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> // " evolutionary analysis. PLoS Computational Biology 10(4): e1003537"</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"> // , year = 2014, firstAuthorSurname = "bouckaert",</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> // DOI="10.1371/journal.pcbi.1003537")</span>
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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">
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-@Citation(value="Bouckaert, Remco, Timothy G. Vaughan, Joëlle Barido-Sottani, Sebastián Duchêne, Mathieu Fourment, \n"</span></span>
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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">
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- + "Alexandra Gavryushkina, Joseph Heled, Graham Jones, Denise Kühnert, Nicola De Maio, Michael Matschiner, \n"</span></span>
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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">
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- + "Fábio K. Mendes, Nicola F. Müller, Huw A. Ogilvie, Louis du Plessis, Alex Popinga, Andrew Rambaut, \n"</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+@Citation(value="Bouckaert, Remco, Timothy G. Vaughan, Joelle Barido-Sottani, Sebastian Duchene, Mathieu Fourment, \n"</span></span>
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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">
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ + "Alexandra Gavryushkina, Joseph Heled, Graham Jones, Denise Kuhnert, Nicola De Maio, Michael Matschiner, \n"</span></span>
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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">
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ + "Fabio K. Mendes, Nicola F. Muller, Huw A. Ogilvie, Louis du Plessis, Alex Popinga, Andrew Rambaut, \n"</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"> + "David Rasmussen, Igor Siveroni, Marc A. Suchard, Chieh-Hsi Wu, Dong Xie, Chi Zhang, Tanja Stadler, \n"</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"> + "Alexei J. Drummond \n"</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"> + " BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis. \n"</span></pre>
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<li id="48145ea6d5b9e8f96496083c8fc5a2df8a675d89">
<a href="https://salsa.debian.org/med-team/beast2-mcmc/-/compare/98151f7c6e58952310a65305316015b227ca4962...5563694f37e510a88cd1af59e7f74c548b4983eb#48145ea6d5b9e8f96496083c8fc5a2df8a675d89"><strong>debian/patches/remove_import_swing_security.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Description: Remove import of unused org.fest.swing.security package</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"> The ExitException class form this package is not used, instead ExitException</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"> if defined in the file as an override of java.lang.SecurityException.</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="p">Author: Pierre Gruet <pgtdebian@free.fr></span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="p">Forwarded: https://github.com/CompEvol/beast2/issues/921</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"><span class="p">Last-Update: 2020-09-15</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff">--- a/src/test/beast/integration/ExampleXmlParsingTest.java</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/test/beast/integration/ExampleXmlParsingTest.java</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"><span class="p">@@ -9,7 +9,6 @@</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> import java.util.ArrayList;</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"> import java.util.List;</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import org.fest.swing.security.ExitException;</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> import org.junit.Test;</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"> import beast.app.beastapp.BeastMain;</span></pre>
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<a href="https://salsa.debian.org/med-team/beast2-mcmc/-/compare/98151f7c6e58952310a65305316015b227ca4962...5563694f37e510a88cd1af59e7f74c548b4983eb#eb03b62356d7a87ac94d69bcbedc01343e93f8a1"><strong>debian/patches/remove_jsign_from_build.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Description: net.jsign is used for WIndows releases, removing it from build.xml</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Author: Pierre Gruet <pgtdebian@free.fr></span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Forwarded: not-needed</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="p">Last-Update: 2020-09-15</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff">--- a/build.xml</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/build.xml</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="p">@@ -293,8 +293,6 @@</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"> <property name="Windows_package_dir" value="${Windows_dir}/${BEAST_name}" /></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- <taskdef name="jsign" classname="net.jsign.JsignTask" classpath="${lib}/jsign-3.1.jar"/></span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"> <!-- Need to either install Launch4j under {BEAST workspace}/${release}</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> or install it in the default directory and change the location of launch4j.dir --></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"> <!--depends="build_jar_all_BEAST_NoJUnitTest"--></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"><span class="p">@@ -365,31 +363,6 @@</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"> --></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"> </launch4j></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-<jsign file="${Windows_package_dir}/${BEAUti_name}.exe"</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- name="BEAUti"</span></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;">- url="http://beast2.org"</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- keystore="keystore.pfx"</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- alias="http://beast2.org"</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- storepass="${storepass}"</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- tsaurl="http://timestamp.comodoca.com/authenticode"/></span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- <!-- BEAST v?.?.?.exe --></span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- <launch4j configFile="${Windows_dir}/BEAST_launch4j.xml"</span></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;">- jar="${dist}/launcher.jar"</span></span>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- outfile="${Windows_package_dir}/${BEAST_name}.exe"</span></span>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- fileVersion="${version_number}.0"</span></span>
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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- txtFileVersion="${version}"</span></span>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- productVersion="${version_number}.0"</span></span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- txtProductVersion="${version}" /></span></span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-<jsign file="${Windows_package_dir}/${BEAST_name}.exe"</span></span>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- name="BEAST"</span></span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- url="http://beast2.org"</span></span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- keystore="keystore.pfx"</span></span>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- alias="http://beast2.org"</span></span>
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43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- storepass="${storepass}"</span></span>
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44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- tsaurl="http://timestamp.comodoca.com/authenticode"/></span></span>
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45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"> <!--<launch4j configFile="${Windows_dir}/TreeStat_launch4j.xml"</span>
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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="diff"> jar="${dist}/beast.jar"</span>
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48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="diff"> outfile="${Windows_package_dir}/${TreeStat_name}.exe"</span>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"><span class="p">@@ -415,14 +388,6 @@</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="diff"> productVersion="${version_number}.0"</span>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="diff"> txtProductVersion="${version}"/></span>
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52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="diff"> </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;">-<jsign file="${Windows_package_dir}/${LogCombiner_name}.exe"</span></span>
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54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- name="LogCombiner"</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;">- url="http://beast2.org"</span></span>
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56
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- keystore="keystore.pfx"</span></span>
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57
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- alias="http://beast2.org"</span></span>
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58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- storepass="${storepass}"</span></span>
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- tsaurl="http://timestamp.comodoca.com/authenticode"/></span></span>
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60
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="diff"> <launch4j configFile="${Windows_dir}/TreeAnnotator_launch4j.xml"</span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="diff"> jar="${dist}/launcher.jar"</span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="diff"> outfile="${Windows_package_dir}/TreeAnnotator.exe"</span>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="diff"><span class="p">@@ -431,14 +396,6 @@</span></span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="diff"> productVersion="${version_number}.0"</span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="diff"> txtProductVersion="${version}"/></span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="diff"> </span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-<jsign file="${Windows_package_dir}/TreeAnnotator.exe"</span></span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- name="TreeAnnotator"</span></span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- url="http://beast2.org"</span></span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- keystore="keystore.pfx"</span></span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- alias="http://beast2.org"</span></span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- storepass="${storepass}"</span></span>
</pre>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- tsaurl="http://timestamp.comodoca.com/authenticode"/></span></span>
</pre>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="diff"> <launch4j configFile="${tools_dir}/DensiTree_launch4j.xml"</span>
</pre>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="diff"> jar="${tools_dir}/DensiTree.jar"</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="78" 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">
78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="diff"> outfile="${Windows_package_dir}/DensiTree.exe"</span>
</pre>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="diff"><span class="p">@@ -447,15 +404,6 @@</span></span>
</pre>
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="diff"> productVersion="2.0.0.0"</span>
</pre>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="diff"> txtProductVersion="2.0.0.0" /></span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="diff"> </span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-<jsign file="${Windows_package_dir}/DensiTree.exe"</span></span>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- name="DensiTree"</span></span>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- url="http://beast2.org"</span></span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- keystore="keystore.pfx"</span></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;">- alias="http://beast2.org"</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;">- storepass="${storepass}"</span></span>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- tsaurl="http://timestamp.comodoca.com/authenticode"/></span></span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="diff"> <launch4j configFile="${Windows_dir}/AppLauncher_launch4j.xml"</span>
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93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="diff"> jar="${dist}/launcher.jar"</span>
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94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="diff"> outfile="${Windows_package_dir}/AppLauncher.exe"</span>
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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="diff"><span class="p">@@ -464,14 +412,6 @@</span></span>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="diff"> productVersion="${version_number}.0"</span>
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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="diff"> txtProductVersion="${version}"/></span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="diff"> </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;">-<jsign file="${Windows_package_dir}/AppLauncher.exe"</span></span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- name="AppLauncher"</span></span>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- url="http://beast2.org"</span></span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- keystore="keystore.pfx"</span></span>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- alias="http://beast2.org"</span></span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- storepass="${storepass}"</span></span>
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- tsaurl="http://timestamp.comodoca.com/authenticode"/></span></span>
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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;">-</span></span>
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="diff"> <copy todir="${Windows_package_dir}/templates/"></span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="diff"> <fileset dir="templates/" /></span>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="diff"> </copy></span>
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="diff"><span class="p">@@ -559,14 +499,6 @@</span></span>
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="diff"> --></span>
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="diff"> </launch4j></span>
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- <jsign file="${Windows_package_dir}/${BEAUti_name}.exe"</span></span>
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115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- name="BEAUti"</span></span>
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116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- url="http://beast2.org"</span></span>
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117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- keystore="keystore.pfx"</span></span>
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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- alias="http://beast2.org"</span></span>
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119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- storepass="${storepass}"</span></span>
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- tsaurl="http://timestamp.comodoca.com/authenticode"/></span></span>
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<pre style="margin: 0;">+<span id="LC121" 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="LC122" class="line" lang="diff"> <!-- BEAST v?.?.?.exe --></span>
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="diff"> <launch4j configFile="${Windows_dir}/BEAST_launch4j_jre.xml"</span>
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="diff"> jar="${dist}/launcher.jar"</span>
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="diff"><span class="p">@@ -576,14 +508,6 @@</span></span>
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="diff"> productVersion="${version_number}.0"</span>
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="diff"> txtProductVersion="${version}" /></span>
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- <jsign file="${Windows_package_dir}/${BEAST_name}.exe"</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;">- name="BEAST"</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;">- url="http://beast2.org"</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;">- keystore="keystore.pfx"</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;">- alias="http://beast2.org"</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;">- storepass="${storepass}"</span></span>
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135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- tsaurl="http://timestamp.comodoca.com/authenticode"/></span></span>
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136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="diff"> <!--<launch4j configFile="${Windows_dir}/TreeStat_launch4j.xml"</span>
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138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="diff"> jar="${dist}/beast.jar"</span>
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139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="diff"> outfile="${Windows_package_dir}/${TreeStat_name}.exe"</span>
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140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="diff"><span class="p">@@ -609,14 +533,6 @@</span></span>
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141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="diff"> productVersion="${version_number}.0"</span>
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142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="diff"> txtProductVersion="${version}"/></span>
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143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="diff"> </span>
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144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- <jsign file="${Windows_package_dir}/${LogCombiner_name}.exe"</span></span>
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145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- name="LogCombiner"</span></span>
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146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- url="http://beast2.org"</span></span>
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147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- keystore="keystore.pfx"</span></span>
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148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- alias="http://beast2.org"</span></span>
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149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- storepass="${storepass}"</span></span>
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150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- tsaurl="http://timestamp.comodoca.com/authenticode"/></span></span>
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151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="diff"> <launch4j configFile="${Windows_dir}/TreeAnnotator_launch4j_jre.xml"</span>
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153
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="diff"> jar="${dist}/launcher.jar"</span>
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<td class="diff-line-num new new_line" data-linenumber="154" 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">
154
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="diff"> outfile="${Windows_package_dir}/TreeAnnotator.exe"</span>
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<td class="diff-line-num new new_line" data-linenumber="155" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
155
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="diff"><span class="p">@@ -625,14 +541,6 @@</span></span>
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156
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="diff"> productVersion="${version_number}.0"</span>
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157
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="diff"> txtProductVersion="${version}"/></span>
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158
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="diff"> </span>
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159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- <jsign file="${Windows_package_dir}/TreeAnnotator.exe"</span></span>
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160
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- name="TreeAnnotator"</span></span>
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161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- url="http://beast2.org"</span></span>
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162
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- keystore="keystore.pfx"</span></span>
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163
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- alias="http://beast2.org"</span></span>
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164
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- storepass="${storepass}"</span></span>
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165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- tsaurl="http://timestamp.comodoca.com/authenticode"/></span></span>
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166
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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167
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="diff"> <launch4j configFile="${tools_dir}/DensiTree_launch4j_jre.xml"</span>
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168
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="diff"> jar="${tools_dir}/DensiTree.jar"</span>
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169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="diff"> outfile="${Windows_package_dir}/DensiTree.exe"</span>
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170
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="diff"><span class="p">@@ -641,14 +549,6 @@</span></span>
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171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="diff"> productVersion="2.0.0.0"</span>
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172
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="diff"> txtProductVersion="2.0.0.0" /></span>
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173
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="diff"> </span>
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<td class="diff-line-num new new_line" data-linenumber="174" 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">
174
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- <jsign file="${Windows_package_dir}/DensiTree.exe"</span></span>
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<td class="diff-line-num new new_line" data-linenumber="175" 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">
175
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- name="DensiTree"</span></span>
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<td class="diff-line-num new new_line" data-linenumber="176" 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">
176
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- url="http://beast2.org"</span></span>
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<td class="diff-line-num new new_line" data-linenumber="177" 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">
177
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- keystore="keystore.pfx"</span></span>
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<td class="diff-line-num new new_line" data-linenumber="178" 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">
178
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- alias="http://beast2.org"</span></span>
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<td class="diff-line-num new new_line" data-linenumber="179" 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">
179
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- storepass="${storepass}"</span></span>
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- tsaurl="http://timestamp.comodoca.com/authenticode"/></span></span>
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<pre style="margin: 0;">+<span id="LC181" 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="LC182" class="line" lang="diff"> <launch4j configFile="${Windows_dir}/AppLauncher_launch4j_jre.xml"</span>
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<pre style="margin: 0;">+<span id="LC183" class="line" lang="diff"> jar="${dist}/launcher.jar"</span>
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<pre style="margin: 0;">+<span id="LC184" class="line" lang="diff"> outfile="${Windows_package_dir}/AppLauncher.exe"</span>
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<pre style="margin: 0;">+<span id="LC185" class="line" lang="diff"><span class="p">@@ -657,14 +557,6 @@</span></span>
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="diff"> productVersion="${version_number}.0"</span>
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<pre style="margin: 0;">+<span id="LC187" class="line" lang="diff"> txtProductVersion="${version}"/></span>
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<pre style="margin: 0;">+<span id="LC188" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC189" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- <jsign file="${Windows_package_dir}/AppLauncher.exe"</span></span>
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190
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<pre style="margin: 0;">+<span id="LC190" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- name="AppLauncher"</span></span>
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<pre style="margin: 0;">+<span id="LC191" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- url="http://beast2.org"</span></span>
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<pre style="margin: 0;">+<span id="LC192" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- keystore="keystore.pfx"</span></span>
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193
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<pre style="margin: 0;">+<span id="LC193" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- alias="http://beast2.org"</span></span>
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<pre style="margin: 0;">+<span id="LC194" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- storepass="${storepass}"</span></span>
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<pre style="margin: 0;">+<span id="LC195" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- tsaurl="http://timestamp.comodoca.com/authenticode"/></span></span>
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<pre style="margin: 0;">+<span id="LC196" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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197
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<pre style="margin: 0;">+<span id="LC197" class="line" lang="diff"> </span>
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198
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<pre style="margin: 0;">+<span id="LC198" class="line" lang="diff"> <copy todir="${Windows_package_dir}/templates/"></span>
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199
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<pre style="margin: 0;">+<span id="LC199" class="line" lang="diff"> <fileset dir="templates/" /></span></pre>
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<li id="bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
<a href="https://salsa.debian.org/med-team/beast2-mcmc/-/compare/98151f7c6e58952310a65305316015b227ca4962...5563694f37e510a88cd1af59e7f74c548b4983eb#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">@@ -4,3 +4,6 @@ remove_appbundler.patch</td>
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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"># revert_NewickLexer.java_to_antlr_4.5.patch</span>
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5
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5
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">antlr-compatibility.patch</span>
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6
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6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">remove_mac_only_code.patch</span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">remove_jsign_from_build.patch</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">accents_in_source.patch</span>
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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">remove_import_swing_security.patch</span></pre>
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