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<h3 style="margin-top: 20px; margin-bottom: 10px;">
Andreas Tille pushed to branch upstream at <a href="https://salsa.debian.org/med-team/pangolin">Debian Med / pangolin</a>
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Commits:
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<strong style="font-weight: bold;"><a href="https://salsa.debian.org/med-team/pangolin/-/commit/2726a5f55cf63579be66d64c4e2650fe664bb560">2726a5f5</a></strong>
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<span> by Andreas Tille </span> <i> at 2022-12-23T16:18:39+01:00 </i>
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<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 0.8125rem; color: #303030; position: relative; font-family: "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; word-break: break-all; word-wrap: break-word; background-color: #fafafa; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dbdbdb;'>New upstream version 4.1.3</pre>
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30 changed files:
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The diff was not included because it is too large.
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