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<h3>
Pierre Gruet pushed to branch master
at <a href="https://salsa.debian.org/med-team/mauve-aligner">Debian Med / mauve-aligner</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/mauve-aligner/-/commit/836cb722e9b0c6a93dc10312ed29678647323bbd">836cb722</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2022-04-10T21:24:43+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Depending on biojava-live 1:1.9.5+dfsg-1, which introduced new jar names
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/mauve-aligner/-/commit/bb898c47d86a2330f50e9d33b06b0784f7b94ca8">bb898c47</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2022-04-10T21:24:54+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Refreshing patches
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/mauve-aligner/-/commit/0cd3965cf2596060e8d307527311ca0796cddbd9">0cd3965c</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2022-04-10T21:25:31+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Setting the package to be 'Architecture: all'
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/mauve-aligner/-/commit/404cf94b70c1ef5d919986e7f4a8b950b7b5d77b">404cf94b</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2022-04-10T21:26:20+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Raising Standards version to 4.6.0 (no change)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/mauve-aligner/-/commit/81c2b2996e4a6b024c25aae8e4b01e7b753c6a13">81c2b299</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2022-04-10T21:31:04+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Updating changelog
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/mauve-aligner/-/commit/445eac1df11e5f9553025361d42efeb45178bd94">445eac1d</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2022-04-10T21:54:26+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Remove -1 in versioned build-depend
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/mauve-aligner/-/commit/de562ce93d63d0af41658d314effdd546b28262b">de562ce9</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2022-04-10T22:52:02+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Upload to experimental
</pre>
</li>
</ul>
<h4>8 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
</a>
</li>
<li class="file-stats">
<a href="#09661b26dadd0f6da66651a045417e1c81207c10">
debian/manifest
</a>
</li>
<li class="file-stats">
<a href="#d9a9f23c4683d1cf1a8b3c512f017d61a87c6b59">
debian/patches/debian_classes.patch
</a>
</li>
<li class="file-stats">
<a href="#93def4fb7ec48e4d40901892595b6ac85d36babe">
debian/patches/do_not_use_goose_jar.patch
</a>
</li>
<li class="file-stats">
<a href="#e99fbbbe536c1d5f83865f27f3f12b0f43e1ab33">
debian/patches/java17-compatibility.patch
</a>
</li>
<li class="file-stats">
<a href="#e8c7ba89aef1291ae2736d3b35f71a3bbe771cbf">
debian/patches/no_ext_dir_at_all.patch
</a>
</li>
<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
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</li>
</ul>
<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/mauve-aligner/-/compare/0698f54062f9113494e21fb0cfc6219dd4969f6f...de562ce93d63d0af41658d314effdd546b28262b#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">mauve-aligner (2.4.0+4736-5) experimental; urgency=medium</span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
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<td class="new_line diff-line-num new" 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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * Team upload.</span>
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<td class="new_line diff-line-num new" data-linenumber="4" 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="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> * Depending on biojava-live 1:1.9.5+dfsg, which introduced new jar names</span>
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<td class="new_line diff-line-num new" data-linenumber="5" 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="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> * Refreshing patches</span>
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<td class="new_line diff-line-num new" data-linenumber="6" 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="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> * Setting the package to be 'Architecture: all'</span>
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<td class="new_line diff-line-num new" 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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> * Raising Standards version to 4.6.0 (no change)</span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> -- Pierre Gruet <pgt@debian.org> Sun, 10 Apr 2022 21:54:44 +0200</span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">mauve-aligner (2.4.0+4736-4) unstable; urgency=medium</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"> * Team upload.</span>
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<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/mauve-aligner/-/compare/0698f54062f9113494e21fb0cfc6219dd4969f6f...de562ce93d63d0af41658d314effdd546b28262b#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="9" 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="diff-line-num unfold js-unfold new_line" data-linenumber="9" 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">@@ -9,24 +9,24 @@ Build-Depends: debhelper-compat (= 13),</td>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> ant,</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> ant-contrib,</span>
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<td class="new_line diff-line-num" data-linenumber="11" 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">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> junit,</span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext"> libbiojava-java,</span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> libbiojava-java<span class="idiff left right addition"> (>= 1:1.9.5+dfsg)</span>,</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"> libcommons-cli-java,</span>
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14
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14
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"> libdbus-java,</span>
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15
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15
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"> libzeus-jscl-java,</span>
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16
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16
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext"> libunixsocket-java,</span>
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17
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17
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext"> imagemagick</span>
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18
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC18" class="line" lang="plaintext">Standards-Version: 4.<span class="idiff left right deletion">5.1</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">Standards-Version: 4.<span class="idiff left right addition">6.0</span></span>
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19
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/mauve-aligner</span>
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20
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/mauve-aligner.git</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext">Homepage: https://darlinglab.org/mauve/</span>
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22
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext">Rules-Requires-Root: no</span>
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23
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext"></span>
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24
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext">Package: mauve-aligner</span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC25" class="line" lang="plaintext">Architecture: a<span class="idiff left right deletion">ny</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">Architecture: a<span class="idiff left right addition">ll</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC26" class="line" lang="plaintext">Depends: ${java:Depends},</span>
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27
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC27" class="line" lang="plaintext"> java-wrappers,</span>
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28
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC28" class="line" lang="plaintext"> ${misc:Depends},</span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC29" class="line" lang="plaintext"> libbiojava-java,</span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext"> libbiojava-java<span class="idiff left right addition"> (>= 1:1.9.5+dfsg-1)</span>,</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC30" class="line" lang="plaintext"> progressivemauve</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC31" class="line" lang="plaintext">Recommends: ${java:Recommends}</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC32" class="line" lang="plaintext">Description: multiple genome alignment</span>
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<a href="https://salsa.debian.org/med-team/mauve-aligner/-/compare/0698f54062f9113494e21fb0cfc6219dd4969f6f...de562ce93d63d0af41658d314effdd546b28262b#09661b26dadd0f6da66651a045417e1c81207c10"><strong>debian/manifest</strong></a>
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1
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">usr/share/java/Mauve.jar:</span>
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2
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<td class="new_line diff-line-num old" data-linenumber="2" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext"> Class-Path: /usr/share/java/biojava.jar /usr/share/java/commons-cli.jar /usr/share/icedtea-web/netx.jar /usr/share/java/zeus-jscl.jar /usr/share/java/dbus.jar /usr/share/java/unix.jar</span></pre></td>
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2
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"> Class-Path: /usr/share/java/biojava<span class="idiff left right addition">-core.jar /usr/share/java/biojava-gui</span>.jar /usr/share/java/commons-cli.jar /usr/share/icedtea-web/netx.jar /usr/share/java/zeus-jscl.jar /usr/share/java/dbus.jar /usr/share/java/unix.jar</span></pre></td>
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<a href="https://salsa.debian.org/med-team/mauve-aligner/-/compare/0698f54062f9113494e21fb0cfc6219dd4969f6f...de562ce93d63d0af41658d314effdd546b28262b#d9a9f23c4683d1cf1a8b3c512f017d61a87c6b59"><strong>debian/patches/debian_classes.patch</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">@@ -23,7 +23,7 @@ Description: Use Debian packaged classes</td>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC23" class="line" lang="diff"> </classpath></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC24" class="line" lang="diff"> </taskdef></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC25" class="line" lang="diff"> </span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC26" class="line" lang="diff"><span class="p">@@ -77,17 +78,1<span class="idiff left right deletion">4</span> @@</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"><span class="p">@@ -77,17 +78,1<span class="idiff left right addition">5</span> @@</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC27" class="line" lang="diff"> <!-- Build all java source files --></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC28" class="line" lang="diff"> <javac</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC29" class="line" lang="diff"> classpath="</span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="31" 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">@@ -31,7 +31,8 @@ Description: Use Debian packaged classes</td>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC31" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- ${ext}/bytecode-1.9.2-SNAPSHOT.jar;</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC32" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- ${ext}/gui-1.9.2-SNAPSHOT.jar;</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC33" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- ${ext}/commons-cli-1.2.jar;</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ ${deblib}/biojava-core.jar;</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ ${deblib}/biojava-gui.jar;</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC36" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ ${deblib}/commons-cli.jar;</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC37" class="line" lang="diff"> ${support}/junit.jar;</span>
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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">@@ -49,7 +50,7 @@ Description: Use Debian packaged classes</td>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC50" class="line" lang="diff"> target="1.6"</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC51" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/.classpath</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC52" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/.classpath</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC54" class="line" lang="diff"> <classpathentry kind="src" path="src"/></span>
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55
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC55" class="line" lang="diff"> <classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER"/></span>
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56
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC56" class="line" lang="diff"> <classpathentry kind="var" path="JUNIT_HOME/junit.jar" sourcepath="ECLIPSE_HOME/plugins/org.eclipse.jdt.source_3.0.0/src/org.junit_3.8.1/junitsrc.zip"/></span>
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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">@@ -72,6 +73,7 @@ Description: Use Debian packaged classes</td>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC73" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- <classpathentry kind="lib" path="ext/core-1.9.2-SNAPSHOT.jar"/></span></span>
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74
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC74" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- <classpathentry kind="lib" path="ext/gui-1.9.2-SNAPSHOT.jar"/></span></span>
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74
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75
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC75" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ <classpathentry kind="lib" path="/usr/share/icedtea-web/netx.jar"/></span></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC75" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ <classpathentry kind="lib" path="/usr/share/java/biojava.jar"/></span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC76" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ <classpathentry kind="lib" path="/usr/share/java/biojava-core.jar"/></span></span>
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77
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC77" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ <classpathentry kind="lib" path="/usr/share/java/biojava-gui.jar"/></span></span>
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78
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC78" class="line" lang="diff"> <classpathentry kind="output" path="bin"/></span>
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77
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79
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC79" class="line" lang="diff"> </classpath></span></pre></td>
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<li id="93def4fb7ec48e4d40901892595b6ac85d36babe">
<a href="https://salsa.debian.org/med-team/mauve-aligner/-/compare/0698f54062f9113494e21fb0cfc6219dd4969f6f...de562ce93d63d0af41658d314effdd546b28262b#93def4fb7ec48e4d40901892595b6ac85d36babe"><strong>debian/patches/do_not_use_goose_jar.patch</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="11" 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">@@ -11,11 +11,11 @@ Description: Do not use goose.jar since it is not used accorcing to upstream</td>
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11
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11
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC11" class="line" lang="diff"> <classpathentry kind="lib" path="/usr/share/java/unix.jar"/></span>
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12
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC12" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- <classpathentry kind="lib" path="ext/goose.jar"/></span></span>
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13
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC13" class="line" lang="diff"> <classpathentry kind="lib" path="/usr/share/icedtea-web/netx.jar"/></span>
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14
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC14" class="line" lang="diff"> <classpathentry kind="lib" path="/usr/share/java/biojava.jar"/></span>
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15
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC15" class="line" lang="diff"> <classpathentry kind="<span class="idiff left deletion">output</span>" path="<span class="idiff right deletion">bin</span>"/></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"> <classpathentry kind="lib" path="/usr/share/java/biojava<span class="idiff left right addition">-core</span>.jar"/></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> <classpathentry kind="<span class="idiff left addition">lib</span>" path="<span class="idiff right addition">/usr/share/java/biojava-gui.jar</span>"/></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC16" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/build.xml</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC17" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/build.xml</span></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC18" class="line" lang="diff"><span class="p">@@ -8<span class="idiff left deletion">2</span>,7 +8<span class="idiff right deletion">2</span>,6 @@</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"><span class="p">@@ -8<span class="idiff left addition">3</span>,7 +8<span class="idiff right addition">3</span>,6 @@</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC19" class="line" lang="diff"> ${deblib}/commons-cli.jar;</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC20" class="line" lang="diff"> ${support}/junit.jar;</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC21" class="line" lang="diff"> ${deblib}/zeus-jscl.jar;</span>
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<a href="https://salsa.debian.org/med-team/mauve-aligner/-/compare/0698f54062f9113494e21fb0cfc6219dd4969f6f...de562ce93d63d0af41658d314effdd546b28262b#e99fbbbe536c1d5f83865f27f3f12b0f43e1ab33"><strong>debian/patches/java17-compatibility.patch</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">@@ -3,7 +3,7 @@ Author: Emmanuel Bourg <ebourg@apache.org></td>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC3" class="line" lang="diff"><span class="p">Forwarded: no</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC4" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/build.xml</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC5" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/build.xml</span></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC6" class="line" lang="diff"><span class="p">@@ -10<span class="idiff left deletion">2</span>,7 +10<span class="idiff right deletion">2</span>,7 @@</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"><span class="p">@@ -10<span class="idiff left addition">3</span>,7 +10<span class="idiff right addition">3</span>,7 @@</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC7" class="line" lang="diff"> <rmic base="${build}" classname="org.gel.mauve.remote.RemoteControlImpl" /></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC8" class="line" lang="diff"> </target></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC9" class="line" lang="diff"> </span>
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<a href="https://salsa.debian.org/med-team/mauve-aligner/-/compare/0698f54062f9113494e21fb0cfc6219dd4969f6f...de562ce93d63d0af41658d314effdd546b28262b#e8c7ba89aef1291ae2736d3b35f71a3bbe771cbf"><strong>debian/patches/no_ext_dir_at_all.patch</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">@@ -14,7 +14,7 @@ Description: Some remainings of mentioning ext/ in build.xml were breaking</td>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC14" class="line" lang="diff"> <property name="deblib" location="/usr/share/java" /></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC15" class="line" lang="diff"> <property name="support" location="/usr/share/java"/></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC16" class="line" lang="diff"> </span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC17" class="line" lang="diff"><span class="p">@@ -10<span class="idiff left deletion">4</span>,18 +10<span class="idiff right deletion">3</span>,6 @@</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"><span class="p">@@ -10<span class="idiff left addition">5</span>,18 +10<span class="idiff right addition">4</span>,6 @@</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC18" class="line" lang="diff"> </target></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC20" class="line" lang="diff"> <target name="jar" depends="rmic"></span>
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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">@@ -33,7 +33,7 @@ Description: Some remainings of mentioning ext/ in build.xml were breaking</td>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC33" class="line" lang="diff"> </span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC34" class="line" lang="diff"> <!-- Put everything in ${build} into the Mauve.jar file --></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC35" class="line" lang="diff"> <delete file="Mauve.jar"/></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC36" class="line" lang="diff"><span class="p">@@ -12<span class="idiff left deletion">6</span>,7 +11<span class="idiff right deletion">3</span>,6 @@</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC37" class="line" lang="diff"> <manifest></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC38" class="line" lang="diff"> <attribute name="Main-Class" value="org.gel.mauve.gui.Mauve"/></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC39" class="line" lang="diff"> <attribute name="Built-By" value="${user.name}"/></span>
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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">@@ -41,7 +41,7 @@ Description: Some remainings of mentioning ext/ in build.xml were breaking</td>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC41" class="line" lang="diff"> <section name="common"></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC42" class="line" lang="diff"> <attribute name="Specification-Title" value="Mauve"/></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC43" class="line" lang="diff"> <attribute name="Specification-Version" value="${version}"/></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC44" class="line" lang="diff"><span class="p">@@ -16<span class="idiff left deletion">1</span>,14 +14<span class="idiff right deletion">7</span>,6 @@</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"><span class="p">@@ -16<span class="idiff left addition">2</span>,14 +14<span class="idiff right addition">8</span>,6 @@</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC45" class="line" lang="diff"> <signjar jar="mauveApplet.jar" alias="${key.alias}" storepass="${key.password}" keystore="${key.keystore}" /></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC47" class="line" lang="diff"> </span>
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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">@@ -56,7 +56,7 @@ Description: Some remainings of mentioning ext/ in build.xml were breaking</td>
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56
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC56" class="line" lang="diff"> <target name="testdist" depends="signjars"></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC57" class="line" lang="diff"> <copy todir="C:\htdocs" file="Mauve.jar" /></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC58" class="line" lang="diff"> <copy todir="C:\htdocs" file="mauveApplet.jar" /></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC59" class="line" lang="diff"><span class="p">@@ -20<span class="idiff left deletion">5</span>,7 +18<span class="idiff right deletion">3</span>,6 @@</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC59" class="line" lang="diff"><span class="p">@@ -20<span class="idiff left addition">6</span>,7 +18<span class="idiff right addition">4</span>,6 @@</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC60" class="line" lang="diff"> <include name="mauveAligner" /></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC61" class="line" lang="diff"> <include name="progressiveMauve" /></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC62" class="line" lang="diff"> </tarfileset></span>
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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">@@ -64,7 +64,7 @@ Description: Some remainings of mentioning ext/ in build.xml were breaking</td>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC67" class="line" lang="diff"><span class="p">@@ -23<span class="idiff left deletion">8</span>,11 +21<span class="idiff right deletion">5</span>,6 @@</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC67" class="line" lang="diff"><span class="p">@@ -23<span class="idiff left addition">9</span>,11 +21<span class="idiff right addition">6</span>,6 @@</span></span>
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68
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC68" class="line" lang="diff"> </span>
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69
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC69" class="line" lang="diff"> <target name="asapResources"></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC70" class="line" lang="diff"> <pathconvert property="asap.resources" pathsep=" "></span>
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<a href="https://salsa.debian.org/med-team/mauve-aligner/-/compare/0698f54062f9113494e21fb0cfc6219dd4969f6f...de562ce93d63d0af41658d314effdd546b28262b#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="9" 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="diff-line-num unfold js-unfold new_line" data-linenumber="9" 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">@@ -9,7 +9,7 @@</td>
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9
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC9" class="line" lang="make"><span class="nv" style="color: #008080;">JAVA_HOME</span> <span class="o" style="font-weight: 600;">:=</span> /usr/lib/jvm/default-java</span>
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10
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC10" class="line" lang="make"></span>
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11
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC11" class="line" lang="make"><span class="nv" style="color: #008080;">DEBJAR</span> <span class="o" style="font-weight: 600;">:=</span> /usr/share/java</span>
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12
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC12" class="line" lang="make"><span class="nv" style="color: #008080;">CLASS_PATH</span> <span class="o" style="font-weight: 600;">:=</span> <span class="nv" style="color: #008080;">$(DEBJAR)</span>/biojava.jar:<span class="nv" style="color: #008080;">$(DEBJAR)</span>/commons-cli.jar:<span class="nv" style="color: #008080;">$(DEBJAR)</span>/dbus.jar:<span class="nv" style="color: #008080;">$(DEBJAR)</span>/jebl.jar:<span class="nv" style="color: #008080;">$(DEBJAR)</span>/zeus-jscl.jar</span>
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<td class="old_line diff-line-num new" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC12" class="line" lang="make"><span class="nv" style="color: #008080;">CLASS_PATH</span> <span class="o" style="font-weight: 600;">:=</span> <span class="nv" style="color: #008080;">$(DEBJAR)</span>/biojava<span class="idiff left addition">-core.jar:</span><span class="nv" style="color: #008080;"><span class="idiff addition">$(DEBJAR)</span></span><span class="idiff right addition">/biojava-gui</span>.jar:<span class="nv" style="color: #008080;">$(DEBJAR)</span>/commons-cli.jar:<span class="nv" style="color: #008080;">$(DEBJAR)</span>/dbus.jar:<span class="nv" style="color: #008080;">$(DEBJAR)</span>/jebl.jar:<span class="nv" style="color: #008080;">$(DEBJAR)</span>/zeus-jscl.jar</span>
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13
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC13" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;">## :$(DEBJAR)/postgresql-jdbc4.jar</span></span>
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14
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC14" class="line" lang="make"></span>
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15
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC15" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># to run the test suite</span></span>
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