New upstream version 3.2+dfsg

* 3.2.0

  - Fixes

    - Increase test timeout for internal testsuite and testiphy.

    - HTML report: don't hide header behind top-bar in Chrome.

  - alignment-smc improvements.

* 3.1.5

  - Fixes

    - Make all programs use shipped libstdc++

    - Make MDS plots handle bp-analyze --subsample

    - Increase test timeouts

    - Correctly write initial alignment for fixed alignment partitions.

    - Don't write "file:" for MDS URLs in HTML report

  - Print citations with pmid and pmcid in help.

  - Add Frequencies.uniform[] function.

  - Print help for 0-argument functions like 'dna'

  - Make SEV handle site-compression.

  - HTML report: print version number + lots of cosmetic improvements.

  - Add new tool tree-tool (and map page, etc.)

  - Change alignments-diff highlight color back to red.

  - Clean up DP matrix code.

* 3.1.4

  - Fix prior on alpha in Rates.gamma

* 3.1.3

  - Fix mean_length prior in RS05 model.

  - Add some more color-schemes for drawing alignments-diff output.

  - Add ferns exon/intro data set.

* 3.1.2

  - Fix a testsuite bug

* 3.1.1

  - Print priors on models in their own section.

<!DOCTYPE book [

<!ENTITY  version        "3.1.4"         >

<!ENTITY  version        "3.2"         >

<!ENTITY  source.file    "bali-phy-&version;.tar.gz"         >

<!ENTITY  linux64.file   "bali-phy-&version;-linux64.tar.gz"         >

	  </listitem>

	</varlistentry>

	<varlistentry>

	  <term>C1.run.json</term>

	  <listitem>

	    <para>JSON file containing information about the command line, models, hostname, start time, etc.</para>

	  </listitem>

	</varlistentry>

      </variablelist>

      <para>For the last two files, each line in these files corresponds to one iteration.</para>