All File Changes

v424_preview to v424_preview2 (2021-11-15 to 2021-11-22) v424

• LICENSE
  • lines changed 43, context: html, text, full: html, text
    e13d75a6e72d627977de49db254580c701485b1c Wed Nov 17 06:15:47 2021 -0800
    cleaning up the license situation a little more, refs #27614
  • lines changed 1, context: html, text, full: html, text
    beba46faf8f7d9125df01839fbc8fc9eed23ae35 Thu Nov 18 05:52:08 2021 -0800
    changes to a few licensing pages after questions from Dan, refs #27614
• confs/asia.hg.conf
  • lines changed 3, context: html, text, full: html, text
    5d982484263083886ba301d45eb43a1951f963e0 Sun Nov 21 01:11:52 2021 -0800
    Installing updated hg.conf files from UCSC servers
• confs/euro.hg.conf
  • lines changed 3, context: html, text, full: html, text
    5d982484263083886ba301d45eb43a1951f963e0 Sun Nov 21 01:11:52 2021 -0800
    Installing updated hg.conf files from UCSC servers
• confs/hgwdev.hg.conf
  • lines changed 8, context: html, text, full: html, text
    5d982484263083886ba301d45eb43a1951f963e0 Sun Nov 21 01:11:52 2021 -0800
    Installing updated hg.conf files from UCSC servers
• confs/rr.hg.conf
  • lines changed 3, context: html, text, full: html, text
    5d982484263083886ba301d45eb43a1951f963e0 Sun Nov 21 01:11:52 2021 -0800
    Installing updated hg.conf files from UCSC servers
• src/LICENSE
  • lines changed 20, context: html, text, full: html, text
    e13d75a6e72d627977de49db254580c701485b1c Wed Nov 17 06:15:47 2021 -0800
    cleaning up the license situation a little more, refs #27614
  • lines changed 2, context: html, text, full: html, text
    beba46faf8f7d9125df01839fbc8fc9eed23ae35 Thu Nov 18 05:52:08 2021 -0800
    changes to a few licensing pages after questions from Dan, refs #27614
  • lines changed 26, context: html, text, full: html, text
    93e587629d6d213790e1ddb9650c1a593cb4902d Fri Nov 19 03:24:06 2021 -0800
    fixing up blat and top level license files a bit more, refs #27614
• src/blat/LICENSE
  • lines changed 2, context: html, text, full: html, text
    93e587629d6d213790e1ddb9650c1a593cb4902d Fri Nov 19 03:24:06 2021 -0800
    fixing up blat and top level license files a bit more, refs #27614
• src/hg/LICENSE
  • lines changed 19, context: html, text, full: html, text
    e13d75a6e72d627977de49db254580c701485b1c Wed Nov 17 06:15:47 2021 -0800
    cleaning up the license situation a little more, refs #27614
  • lines changed 1, context: html, text, full: html, text
    f623e51de3e6b6c49b95c7b67277a3044cd95d11 Thu Nov 18 06:10:53 2021 -0800
    forgot liftOver in one LICENSE file, refs #27614
• src/hg/autoSql/LICENSE
  • lines changed 20, context: html, text, full: html, text
    e13d75a6e72d627977de49db254580c701485b1c Wed Nov 17 06:15:47 2021 -0800
    cleaning up the license situation a little more, refs #27614
• src/hg/autoXml/LICENSE
  • lines changed 20, context: html, text, full: html, text
    e13d75a6e72d627977de49db254580c701485b1c Wed Nov 17 06:15:47 2021 -0800
    cleaning up the license situation a little more, refs #27614
• src/hg/cgilib/LICENSE
  • lines changed 14, context: html, text, full: html, text
    927e0aa76504344d57b1c165207d0527a88855c6 Fri Nov 19 03:32:12 2021 -0800
    Hopefully the last round of fixes to the little license files, refs #27614
• src/hg/das/LICENSE
  • lines changed 18, context: html, text, full: html, text
    e13d75a6e72d627977de49db254580c701485b1c Wed Nov 17 06:15:47 2021 -0800
    cleaning up the license situation a little more, refs #27614
  • lines changed 14, context: html, text, full: html, text
    9bc58644c73868bd9227c6f021801d008a970200 Fri Nov 19 03:03:23 2021 -0800
    fixing all the small LICENSE files that flag protected directories, refs #27614
  • lines changed 8, context: html, text, full: html, text
    927e0aa76504344d57b1c165207d0527a88855c6 Fri Nov 19 03:32:12 2021 -0800
    Hopefully the last round of fixes to the little license files, refs #27614
• src/hg/encode/LICENSE
  • lines changed 18, context: html, text, full: html, text
    e13d75a6e72d627977de49db254580c701485b1c Wed Nov 17 06:15:47 2021 -0800
    cleaning up the license situation a little more, refs #27614
  • lines changed 14, context: html, text, full: html, text
    9bc58644c73868bd9227c6f021801d008a970200 Fri Nov 19 03:03:23 2021 -0800
    fixing all the small LICENSE files that flag protected directories, refs #27614
  • lines changed 8, context: html, text, full: html, text
    927e0aa76504344d57b1c165207d0527a88855c6 Fri Nov 19 03:32:12 2021 -0800
    Hopefully the last round of fixes to the little license files, refs #27614
• src/hg/hgApi/LICENSE
  • lines changed 18, context: html, text, full: html, text
    e13d75a6e72d627977de49db254580c701485b1c Wed Nov 17 06:15:47 2021 -0800
    cleaning up the license situation a little more, refs #27614
  • lines changed 14, context: html, text, full: html, text
    9bc58644c73868bd9227c6f021801d008a970200 Fri Nov 19 03:03:23 2021 -0800
    fixing all the small LICENSE files that flag protected directories, refs #27614
  • lines changed 8, context: html, text, full: html, text
    927e0aa76504344d57b1c165207d0527a88855c6 Fri Nov 19 03:32:12 2021 -0800
    Hopefully the last round of fixes to the little license files, refs #27614
• src/hg/hgCollection/LICENSE
  • lines changed 18, context: html, text, full: html, text
    e13d75a6e72d627977de49db254580c701485b1c Wed Nov 17 06:15:47 2021 -0800
    cleaning up the license situation a little more, refs #27614
  • lines changed 14, context: html, text, full: html, text
    9bc58644c73868bd9227c6f021801d008a970200 Fri Nov 19 03:03:23 2021 -0800
    fixing all the small LICENSE files that flag protected directories, refs #27614
  • lines changed 8, context: html, text, full: html, text
    927e0aa76504344d57b1c165207d0527a88855c6 Fri Nov 19 03:32:12 2021 -0800
    Hopefully the last round of fixes to the little license files, refs #27614
• src/hg/hgFileSearch/LICENSE
  • lines changed 18, context: html, text, full: html, text
    e13d75a6e72d627977de49db254580c701485b1c Wed Nov 17 06:15:47 2021 -0800
    cleaning up the license situation a little more, refs #27614
  • lines changed 14, context: html, text, full: html, text
    9bc58644c73868bd9227c6f021801d008a970200 Fri Nov 19 03:03:23 2021 -0800
    fixing all the small LICENSE files that flag protected directories, refs #27614
  • lines changed 8, context: html, text, full: html, text
    927e0aa76504344d57b1c165207d0527a88855c6 Fri Nov 19 03:32:12 2021 -0800
    Hopefully the last round of fixes to the little license files, refs #27614
• src/hg/hgFileUi/LICENSE
  • lines changed 18, context: html, text, full: html, text
    e13d75a6e72d627977de49db254580c701485b1c Wed Nov 17 06:15:47 2021 -0800
    cleaning up the license situation a little more, refs #27614
  • lines changed 14, context: html, text, full: html, text
    9bc58644c73868bd9227c6f021801d008a970200 Fri Nov 19 03:03:23 2021 -0800
    fixing all the small LICENSE files that flag protected directories, refs #27614
  • lines changed 8, context: html, text, full: html, text
    927e0aa76504344d57b1c165207d0527a88855c6 Fri Nov 19 03:32:12 2021 -0800
    Hopefully the last round of fixes to the little license files, refs #27614
• src/hg/hgGateway/LICENSE
  • lines changed 18, context: html, text, full: html, text
    e13d75a6e72d627977de49db254580c701485b1c Wed Nov 17 06:15:47 2021 -0800
    cleaning up the license situation a little more, refs #27614
  • lines changed 14, context: html, text, full: html, text
    9bc58644c73868bd9227c6f021801d008a970200 Fri Nov 19 03:03:23 2021 -0800
    fixing all the small LICENSE files that flag protected directories, refs #27614
  • lines changed 8, context: html, text, full: html, text
    927e0aa76504344d57b1c165207d0527a88855c6 Fri Nov 19 03:32:12 2021 -0800
    Hopefully the last round of fixes to the little license files, refs #27614
• src/hg/hgGene/LICENSE
  • lines changed 18, context: html, text, full: html, text
    e13d75a6e72d627977de49db254580c701485b1c Wed Nov 17 06:15:47 2021 -0800
    cleaning up the license situation a little more, refs #27614
  • lines changed 14, context: html, text, full: html, text
    9bc58644c73868bd9227c6f021801d008a970200 Fri Nov 19 03:03:23 2021 -0800
    fixing all the small LICENSE files that flag protected directories, refs #27614
  • lines changed 8, context: html, text, full: html, text
    927e0aa76504344d57b1c165207d0527a88855c6 Fri Nov 19 03:32:12 2021 -0800
    Hopefully the last round of fixes to the little license files, refs #27614
• src/hg/hgGenome/LICENSE
  • lines changed 18, context: html, text, full: html, text
    e13d75a6e72d627977de49db254580c701485b1c Wed Nov 17 06:15:47 2021 -0800
    cleaning up the license situation a little more, refs #27614
  • lines changed 14, context: html, text, full: html, text
    9bc58644c73868bd9227c6f021801d008a970200 Fri Nov 19 03:03:23 2021 -0800
    fixing all the small LICENSE files that flag protected directories, refs #27614
  • lines changed 8, context: html, text, full: html, text
    927e0aa76504344d57b1c165207d0527a88855c6 Fri Nov 19 03:32:12 2021 -0800
    Hopefully the last round of fixes to the little license files, refs #27614
• src/hg/hgIntegrator/LICENSE
  • lines changed 18, context: html, text, full: html, text
    e13d75a6e72d627977de49db254580c701485b1c Wed Nov 17 06:15:47 2021 -0800
    cleaning up the license situation a little more, refs #27614
  • lines changed 14, context: html, text, full: html, text
    9bc58644c73868bd9227c6f021801d008a970200 Fri Nov 19 03:03:23 2021 -0800
    fixing all the small LICENSE files that flag protected directories, refs #27614
  • lines changed 8, context: html, text, full: html, text
    927e0aa76504344d57b1c165207d0527a88855c6 Fri Nov 19 03:32:12 2021 -0800
    Hopefully the last round of fixes to the little license files, refs #27614
• src/hg/hgPal/LICENSE
  • lines changed 18, context: html, text, full: html, text
    e13d75a6e72d627977de49db254580c701485b1c Wed Nov 17 06:15:47 2021 -0800
    cleaning up the license situation a little more, refs #27614
  • lines changed 14, context: html, text, full: html, text
    9bc58644c73868bd9227c6f021801d008a970200 Fri Nov 19 03:03:23 2021 -0800
    fixing all the small LICENSE files that flag protected directories, refs #27614
  • lines changed 8, context: html, text, full: html, text
    927e0aa76504344d57b1c165207d0527a88855c6 Fri Nov 19 03:32:12 2021 -0800
    Hopefully the last round of fixes to the little license files, refs #27614
• src/hg/hgPcr/LICENSE
  • lines changed 18, context: html, text, full: html, text
    e13d75a6e72d627977de49db254580c701485b1c Wed Nov 17 06:15:47 2021 -0800
    cleaning up the license situation a little more, refs #27614
  • lines changed 14, context: html, text, full: html, text
    9bc58644c73868bd9227c6f021801d008a970200 Fri Nov 19 03:03:23 2021 -0800
    fixing all the small LICENSE files that flag protected directories, refs #27614
  • lines changed 8, context: html, text, full: html, text
    927e0aa76504344d57b1c165207d0527a88855c6 Fri Nov 19 03:32:12 2021 -0800
    Hopefully the last round of fixes to the little license files, refs #27614
• src/hg/hgPhyloPlace/LICENSE
  • lines changed 18, context: html, text, full: html, text
    e13d75a6e72d627977de49db254580c701485b1c Wed Nov 17 06:15:47 2021 -0800
    cleaning up the license situation a little more, refs #27614
  • lines changed 14, context: html, text, full: html, text
    9bc58644c73868bd9227c6f021801d008a970200 Fri Nov 19 03:03:23 2021 -0800
    fixing all the small LICENSE files that flag protected directories, refs #27614
  • lines changed 8, context: html, text, full: html, text
    927e0aa76504344d57b1c165207d0527a88855c6 Fri Nov 19 03:32:12 2021 -0800
    Hopefully the last round of fixes to the little license files, refs #27614
• src/hg/hgPhyloPlace/runUsher.c
  • lines changed 2, context: html, text, full: html, text
    22d4d158752454901bc830d09c32e5b0411a1def Fri Nov 12 17:17:49 2021 -0800
    Ignore new usher output file placement_stats.tsv.
• src/hg/hgPublicSessions/LICENSE
  • lines changed 18, context: html, text, full: html, text
    e13d75a6e72d627977de49db254580c701485b1c Wed Nov 17 06:15:47 2021 -0800
    cleaning up the license situation a little more, refs #27614
  • lines changed 14, context: html, text, full: html, text
    9bc58644c73868bd9227c6f021801d008a970200 Fri Nov 19 03:03:23 2021 -0800
    fixing all the small LICENSE files that flag protected directories, refs #27614
  • lines changed 8, context: html, text, full: html, text
    927e0aa76504344d57b1c165207d0527a88855c6 Fri Nov 19 03:32:12 2021 -0800
    Hopefully the last round of fixes to the little license files, refs #27614
• src/hg/hgSession/LICENSE
  • lines changed 18, context: html, text, full: html, text
    e13d75a6e72d627977de49db254580c701485b1c Wed Nov 17 06:15:47 2021 -0800
    cleaning up the license situation a little more, refs #27614
  • lines changed 14, context: html, text, full: html, text
    9bc58644c73868bd9227c6f021801d008a970200 Fri Nov 19 03:03:23 2021 -0800
    fixing all the small LICENSE files that flag protected directories, refs #27614
  • lines changed 8, context: html, text, full: html, text
    927e0aa76504344d57b1c165207d0527a88855c6 Fri Nov 19 03:32:12 2021 -0800
    Hopefully the last round of fixes to the little license files, refs #27614
• src/hg/hgSuggest/LICENSE
  • lines changed 18, context: html, text, full: html, text
    e13d75a6e72d627977de49db254580c701485b1c Wed Nov 17 06:15:47 2021 -0800
    cleaning up the license situation a little more, refs #27614
  • lines changed 14, context: html, text, full: html, text
    9bc58644c73868bd9227c6f021801d008a970200 Fri Nov 19 03:03:23 2021 -0800
    fixing all the small LICENSE files that flag protected directories, refs #27614
  • lines changed 8, context: html, text, full: html, text
    927e0aa76504344d57b1c165207d0527a88855c6 Fri Nov 19 03:32:12 2021 -0800
    Hopefully the last round of fixes to the little license files, refs #27614
• src/hg/hgTables/LICENSE
  • lines changed 18, context: html, text, full: html, text
    e13d75a6e72d627977de49db254580c701485b1c Wed Nov 17 06:15:47 2021 -0800
    cleaning up the license situation a little more, refs #27614
  • lines changed 14, context: html, text, full: html, text
    9bc58644c73868bd9227c6f021801d008a970200 Fri Nov 19 03:03:23 2021 -0800
    fixing all the small LICENSE files that flag protected directories, refs #27614
  • lines changed 8, context: html, text, full: html, text
    927e0aa76504344d57b1c165207d0527a88855c6 Fri Nov 19 03:32:12 2021 -0800
    Hopefully the last round of fixes to the little license files, refs #27614
• src/hg/hgTables/maf.c
  • lines changed 3, context: html, text, full: html, text
    45eded6990186ff6cb0c8674c9265bfd6fc90390 Mon Nov 15 15:17:29 2021 -0800
    some tweaks to allow bigMaf's that are children to be output as MAF in table browser
  • lines changed 20, context: html, text, full: html, text
    6aaa041c6e3cea383a6ca3275144f6998613cec6 Thu Nov 18 17:34:47 2021 -0800
    be a lot smarter about how we parse bigMaf files. We were opening the file on every bed item, which for bigMaf is about one per base refs #28534
• src/hg/hgTrackUi/LICENSE
  • lines changed 18, context: html, text, full: html, text
    e13d75a6e72d627977de49db254580c701485b1c Wed Nov 17 06:15:47 2021 -0800
    cleaning up the license situation a little more, refs #27614
  • lines changed 14, context: html, text, full: html, text
    9bc58644c73868bd9227c6f021801d008a970200 Fri Nov 19 03:03:23 2021 -0800
    fixing all the small LICENSE files that flag protected directories, refs #27614
  • lines changed 8, context: html, text, full: html, text
    927e0aa76504344d57b1c165207d0527a88855c6 Fri Nov 19 03:32:12 2021 -0800
    Hopefully the last round of fixes to the little license files, refs #27614
• src/hg/hgTracks/LICENSE
  • lines changed 18, context: html, text, full: html, text
    e13d75a6e72d627977de49db254580c701485b1c Wed Nov 17 06:15:47 2021 -0800
    cleaning up the license situation a little more, refs #27614
  • lines changed 14, context: html, text, full: html, text
    9bc58644c73868bd9227c6f021801d008a970200 Fri Nov 19 03:03:23 2021 -0800
    fixing all the small LICENSE files that flag protected directories, refs #27614
  • lines changed 8, context: html, text, full: html, text
    927e0aa76504344d57b1c165207d0527a88855c6 Fri Nov 19 03:32:12 2021 -0800
    Hopefully the last round of fixes to the little license files, refs #27614
• src/hg/hgVai/LICENSE
  • lines changed 18, context: html, text, full: html, text
    e13d75a6e72d627977de49db254580c701485b1c Wed Nov 17 06:15:47 2021 -0800
    cleaning up the license situation a little more, refs #27614
  • lines changed 14, context: html, text, full: html, text
    9bc58644c73868bd9227c6f021801d008a970200 Fri Nov 19 03:03:23 2021 -0800
    fixing all the small LICENSE files that flag protected directories, refs #27614
  • lines changed 8, context: html, text, full: html, text
    927e0aa76504344d57b1c165207d0527a88855c6 Fri Nov 19 03:32:12 2021 -0800
    Hopefully the last round of fixes to the little license files, refs #27614
• src/hg/hgc/LICENSE
  • lines changed 18, context: html, text, full: html, text
    e13d75a6e72d627977de49db254580c701485b1c Wed Nov 17 06:15:47 2021 -0800
    cleaning up the license situation a little more, refs #27614
  • lines changed 14, context: html, text, full: html, text
    9bc58644c73868bd9227c6f021801d008a970200 Fri Nov 19 03:03:23 2021 -0800
    fixing all the small LICENSE files that flag protected directories, refs #27614
  • lines changed 8, context: html, text, full: html, text
    927e0aa76504344d57b1c165207d0527a88855c6 Fri Nov 19 03:32:12 2021 -0800
    Hopefully the last round of fixes to the little license files, refs #27614
• src/hg/hgc/hgc.c
  • lines changed 35, context: html, text, full: html, text
    7e5840e03baf4a7b7c198016c393d0b86f7b72b6 Tue Nov 16 15:25:19 2021 -0800
    allow hgc pages on chains to provide a link to the "other" browser if the other assembly is an unattached genark assembly hub
• src/hg/htdocs/FAQ/FAQlicense.html
  • lines changed 21, context: html, text, full: html, text
    beba46faf8f7d9125df01839fbc8fc9eed23ae35 Thu Nov 18 05:52:08 2021 -0800
    changes to a few licensing pages after questions from Dan, refs #27614
• src/hg/htdocs/goldenPath/help/customTrackText.html
  • lines changed 31, context: html, text, full: html, text
    23857d666cc77fa7c5510f2d9b85824207e28cc0 Fri Nov 19 06:05:16 2021 -0800
    doc'ing incognito mode, refs #28520
• src/hg/htdocs/goldenPath/help/hgSessionHelp.html
  • lines changed 3, context: html, text, full: html, text
    9da877781f5885aacc00721c600130791796b839 Thu Nov 18 18:14:18 2021 -0800
    added link to prove NAR wants browser content
• src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html
  • lines changed 1, context: html, text, full: html, text
    f7d59ef7d3fa01190ef19b00b9efd834e2ccc002 Mon Nov 15 16:15:47 2021 -0800
    Adjusting h4 to h6 to have a titled paragraph as per our example.html, thanks to Gerardo in CR refs #28508
• src/hg/htdocs/goldenPath/help/mirrorManual.html
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    6dd4b07138eb8f479cc4205036c9d6a1794a9f80 Mon Nov 15 13:30:07 2021 -0800
    Add domain exceptions whitelist for allowing us to configure a small number of exceptions that are old servers that are still incompatible with openssl. hg.conf setting httpsCertCheckDomainExceptions or env var https_cert_check_domain_exceptions. This setting is not intended to be used for new servers which should just be advised on correct openssl compatibility, which usually means getting their server to output their intermediate certs as well, or even the cert chain which is typically just 3 certs. refs #28458
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    f90dad3fd12f2d38f0407507297343d692a56a48 Fri Nov 19 14:42:03 2021 -0800
    Adding log setting to httpsCertCheck and making it the new default. This makes it even softer on users, gives us more time to prepare, only logs certs to stderr and only if run as a CGI so that SCRIPT_NAME env var is set. The user does not see anything diffent in behavior and output for log level, but we see cert issues in the log.
• src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
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    83ae9505888aff4bf0d4a06e2e981e46ac41f1e4 Tue Nov 16 15:42:02 2021 -0800
    Clarifying that filters require at least a bed5 to work. Refs #28501
• src/hg/htdocs/goldenPath/newsarch.html
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    97ef58e1e906978d699e48c06fd4081346145eac Mon Nov 15 14:57:56 2021 -0800
    Adding indexNews post and reducing image width refs #28378
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    f62aa226f6a71cd45b275b0b3af091dee100d9ba Wed Nov 17 14:46:46 2021 -0800
    Adding missing url for Fetal Gene Atlas.
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    f34254b679072a80ece69e5e0bd0ec6433c68a09 Wed Nov 17 15:06:26 2021 -0800
    Small edit.
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    e2867e617ae5d61bde6bf4cef1914825244ba645 Thu Nov 18 09:54:21 2021 -0800
    Announcing the Orphadata tracks refs #14319
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    cae3bcce4e68c65d313241df56cae803d584c7d3 Thu Nov 18 10:56:59 2021 -0800
    Fixing typos and adding additional credit refs #14319
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    754e533ae2a773365fbd26d1db114d079659a001 Thu Nov 18 14:26:09 2021 -0800
    Last edits before announcing orphadata refs #14319
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    8a95aed764ccb186703c52e1fdbf5d2f04b0604a Fri Nov 19 09:18:43 2021 -0800
    Small edit to fix hgTrackUi links to open if you aren't on hg38 no RM
• src/hg/htdocs/images/10.jpg
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    d0b2fa0cd94c4ca3783b2b41202e9797d21077ac Mon Nov 15 16:38:21 2021 -0800
    running jhead -purejpg removes massive amount of unneeded meta data no redmine
• src/hg/htdocs/images/16.jpg
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    d0b2fa0cd94c4ca3783b2b41202e9797d21077ac Mon Nov 15 16:38:21 2021 -0800
    running jhead -purejpg removes massive amount of unneeded meta data no redmine
• src/hg/htdocs/images/17.jpg
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    d0b2fa0cd94c4ca3783b2b41202e9797d21077ac Mon Nov 15 16:38:21 2021 -0800
    running jhead -purejpg removes massive amount of unneeded meta data no redmine
• src/hg/htdocs/images/18.jpg
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    d0b2fa0cd94c4ca3783b2b41202e9797d21077ac Mon Nov 15 16:38:21 2021 -0800
    running jhead -purejpg removes massive amount of unneeded meta data no redmine
• src/hg/htdocs/images/19.jpg
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    d0b2fa0cd94c4ca3783b2b41202e9797d21077ac Mon Nov 15 16:38:21 2021 -0800
    running jhead -purejpg removes massive amount of unneeded meta data no redmine
• src/hg/htdocs/indexNews.html
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    97ef58e1e906978d699e48c06fd4081346145eac Mon Nov 15 14:57:56 2021 -0800
    Adding indexNews post and reducing image width refs #28378
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    e2867e617ae5d61bde6bf4cef1914825244ba645 Thu Nov 18 09:54:21 2021 -0800
    Announcing the Orphadata tracks refs #14319
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    cae3bcce4e68c65d313241df56cae803d584c7d3 Thu Nov 18 10:56:59 2021 -0800
    Fixing typos and adding additional credit refs #14319
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    296e1cf711ee6a976bc103d2573ee4130e851c3b Thu Nov 18 16:57:07 2021 -0800
    Fixing name refs #14318
• src/hg/htdocs/license/index.html
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    d663b5afd451477a8f6c19a84c16363079f111cc Wed Nov 17 06:34:51 2021 -0800
    updating license html page to reflect new license, refs #27614
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    beba46faf8f7d9125df01839fbc8fc9eed23ae35 Thu Nov 18 05:52:08 2021 -0800
    changes to a few licensing pages after questions from Dan, refs #27614
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    94c1a35520847138f6b7ceb9a702022a561e95e4 Thu Nov 18 06:05:43 2021 -0800
    More fixes to the license files, refs #27614
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    487d272cf2cc84aeb4c90bd011cc741d92032861 Thu Nov 18 15:57:39 2021 -0800
    Small fixes to wording, capitalization, tags, and more in license page refs #27614
• src/hg/hubApi/LICENSE
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    e13d75a6e72d627977de49db254580c701485b1c Wed Nov 17 06:15:47 2021 -0800
    cleaning up the license situation a little more, refs #27614
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    9bc58644c73868bd9227c6f021801d008a970200 Fri Nov 19 03:03:23 2021 -0800
    fixing all the small LICENSE files that flag protected directories, refs #27614
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    927e0aa76504344d57b1c165207d0527a88855c6 Fri Nov 19 03:32:12 2021 -0800
    Hopefully the last round of fixes to the little license files, refs #27614
• src/hg/inc/genark.h
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    7e5840e03baf4a7b7c198016c393d0b86f7b72b6 Tue Nov 16 15:25:19 2021 -0800
    allow hgc pages on chains to provide a link to the "other" browser if the other assembly is an unattached genark assembly hub
• src/hg/inc/hubConnect.h
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    7e5840e03baf4a7b7c198016c393d0b86f7b72b6 Tue Nov 16 15:25:19 2021 -0800
    allow hgc pages on chains to provide a link to the "other" browser if the other assembly is an unattached genark assembly hub
• src/hg/lib/cart.c
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    6dd4b07138eb8f479cc4205036c9d6a1794a9f80 Mon Nov 15 13:30:07 2021 -0800
    Add domain exceptions whitelist for allowing us to configure a small number of exceptions that are old servers that are still incompatible with openssl. hg.conf setting httpsCertCheckDomainExceptions or env var https_cert_check_domain_exceptions. This setting is not intended to be used for new servers which should just be advised on correct openssl compatibility, which usually means getting their server to output their intermediate certs as well, or even the cert chain which is typically just 3 certs. refs #28458
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    05d0f5fb35b226685765a28f80ee1ff85444f33a Fri Nov 19 05:47:29 2021 -0800
    Adding "incognito" URL variable which allows external sites to open links to us that do not change any of the settings saved in the user's session. This can be especially useful for hgRenderTracks when used from Javascript. refs #28520
• src/hg/lib/genark.c
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    7e5840e03baf4a7b7c198016c393d0b86f7b72b6 Tue Nov 16 15:25:19 2021 -0800
    allow hgc pages on chains to provide a link to the "other" browser if the other assembly is an unattached genark assembly hub
• src/hg/lib/genark.h
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    7e5840e03baf4a7b7c198016c393d0b86f7b72b6 Tue Nov 16 15:25:19 2021 -0800
    allow hgc pages on chains to provide a link to the "other" browser if the other assembly is an unattached genark assembly hub
• src/hg/lib/hubConnect.c
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    7e5840e03baf4a7b7c198016c393d0b86f7b72b6 Tue Nov 16 15:25:19 2021 -0800
    allow hgc pages on chains to provide a link to the "other" browser if the other assembly is an unattached genark assembly hub
• src/hg/lib/makefile
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    7e5840e03baf4a7b7c198016c393d0b86f7b72b6 Tue Nov 16 15:25:19 2021 -0800
    allow hgc pages on chains to provide a link to the "other" browser if the other assembly is an unattached genark assembly hub
• src/hg/liftOver/LICENSE
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    beba46faf8f7d9125df01839fbc8fc9eed23ae35 Thu Nov 18 05:52:08 2021 -0800
    changes to a few licensing pages after questions from Dan, refs #27614
• src/hg/makeDb/doc/asmHubs/master.run.list
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    98314a95f0bd7c06f4a3e01573642a11abea3d31 Thu Nov 18 14:53:34 2021 -0800
    adding another bakers yeast SK1 refs #28533
• src/hg/makeDb/doc/fungiAsmHub/fungi.orderList.tsv
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    7595c48c018df87f5b31ce011c3136821d93b9d1 Thu Nov 18 14:53:58 2021 -0800
    adding another bakers yeast SK1 refs #28533
• src/hg/makeDb/trackDb/cpgIslandSuper.html
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    c572830f58d57d62ce6d87db55efeedaa5bf6f7a Wed Nov 17 10:51:49 2021 -0800
    add note about the calculation command and where to obtain source for the program refs #28401
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
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    0db712dee5613afb52c35deaad27ec64c0eb4646 Fri Nov 19 12:17:51 2021 -0800
    move UCSC Genes back into place
• src/hg/makeDb/trackDb/human/hg38/bloodHao.ra
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    bbc4afc559d3f1914e8a9847ebd2cace27391a61 Mon Nov 15 15:16:29 2021 -0800
    Adding pennantIcons to single-cell tracks refs #28378
• src/hg/makeDb/trackDb/human/hg38/colonWang.ra
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    bbc4afc559d3f1914e8a9847ebd2cace27391a61 Mon Nov 15 15:16:29 2021 -0800
    Adding pennantIcons to single-cell tracks refs #28378
• src/hg/makeDb/trackDb/human/hg38/cortexVelmeshev.ra
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    bbc4afc559d3f1914e8a9847ebd2cace27391a61 Mon Nov 15 15:16:29 2021 -0800
    Adding pennantIcons to single-cell tracks refs #28378
• src/hg/makeDb/trackDb/human/hg38/fetalGeneAtlas.ra
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    bbc4afc559d3f1914e8a9847ebd2cace27391a61 Mon Nov 15 15:16:29 2021 -0800
    Adding pennantIcons to single-cell tracks refs #28378
• src/hg/makeDb/trackDb/human/hg38/heartCellAtlas.ra
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    bbc4afc559d3f1914e8a9847ebd2cace27391a61 Mon Nov 15 15:16:29 2021 -0800
    Adding pennantIcons to single-cell tracks refs #28378
• src/hg/makeDb/trackDb/human/hg38/ileumWang.ra
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    bbc4afc559d3f1914e8a9847ebd2cace27391a61 Mon Nov 15 15:16:29 2021 -0800
    Adding pennantIcons to single-cell tracks refs #28378
• src/hg/makeDb/trackDb/human/hg38/kidneyStewart.ra
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    bbc4afc559d3f1914e8a9847ebd2cace27391a61 Mon Nov 15 15:16:29 2021 -0800
    Adding pennantIcons to single-cell tracks refs #28378
• src/hg/makeDb/trackDb/human/hg38/liverMacParland.html
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    6c4478a57ec213ffa5e89bd48be84fcc8e475e5d Fri Nov 19 09:00:35 2021 -0800
    Fixing link to UCSC Cell Browser for liverMacParland dataset.
• src/hg/makeDb/trackDb/human/hg38/liverMacParland.ra
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    bbc4afc559d3f1914e8a9847ebd2cace27391a61 Mon Nov 15 15:16:29 2021 -0800
    Adding pennantIcons to single-cell tracks refs #28378
• src/hg/makeDb/trackDb/human/hg38/lungTravaglini2020.html
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    23dc9f37e509a39ec7b0e5db387738c7b1121805 Fri Nov 19 09:07:19 2021 -0800
    Fixing link to UCSC Cell Browser for lungTravaglini2020 dataset.
• src/hg/makeDb/trackDb/human/hg38/lungTravaglini2020.ra
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    bbc4afc559d3f1914e8a9847ebd2cace27391a61 Mon Nov 15 15:16:29 2021 -0800
    Adding pennantIcons to single-cell tracks refs #28378
• src/hg/makeDb/trackDb/human/hg38/muscleDeMicheli.html
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    5a971cce3fbacdb85fabbd44b1ef165c08ac3202 Fri Nov 19 08:51:27 2021 -0800
    Fixing link to UCSC Cell Browser for muscleDeMicheli dataset.
• src/hg/makeDb/trackDb/human/hg38/muscleDeMicheli.ra
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    bbc4afc559d3f1914e8a9847ebd2cace27391a61 Mon Nov 15 15:16:29 2021 -0800
    Adding pennantIcons to single-cell tracks refs #28378
• src/hg/makeDb/trackDb/human/hg38/pancreasBaron.html
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    75db31fccb94ec4bfa6edeb9aa44778f76285828 Fri Nov 19 09:16:23 2021 -0800
    Fixing links to UCSC Cell Browser for datasets.
• src/hg/makeDb/trackDb/human/hg38/pancreasBaron.ra
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    bbc4afc559d3f1914e8a9847ebd2cace27391a61 Mon Nov 15 15:16:29 2021 -0800
    Adding pennantIcons to single-cell tracks refs #28378
• src/hg/makeDb/trackDb/human/hg38/placentaVentoTormo.html
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    75db31fccb94ec4bfa6edeb9aa44778f76285828 Fri Nov 19 09:16:23 2021 -0800
    Fixing links to UCSC Cell Browser for datasets.
• src/hg/makeDb/trackDb/human/hg38/placentaVentoTormo.ra
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    bbc4afc559d3f1914e8a9847ebd2cace27391a61 Mon Nov 15 15:16:29 2021 -0800
    Adding pennantIcons to single-cell tracks refs #28378
• src/hg/makeDb/trackDb/human/hg38/rectumWang.html
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    17703b42cd02cfb52687fd646e12d3a79068c938 Fri Nov 19 08:56:04 2021 -0800
    Fixing link to UCSC Cell Browser for rectumWang dataset.
• src/hg/makeDb/trackDb/human/hg38/rectumWang.ra
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    bbc4afc559d3f1914e8a9847ebd2cace27391a61 Mon Nov 15 15:16:29 2021 -0800
    Adding pennantIcons to single-cell tracks refs #28378
• src/hg/makeDb/trackDb/human/hg38/skinSoleBoldo.html
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    75db31fccb94ec4bfa6edeb9aa44778f76285828 Fri Nov 19 09:16:23 2021 -0800
    Fixing links to UCSC Cell Browser for datasets.
• src/hg/makeDb/trackDb/human/hg38/skinSoleBoldo.ra
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    bbc4afc559d3f1914e8a9847ebd2cace27391a61 Mon Nov 15 15:16:29 2021 -0800
    Adding pennantIcons to single-cell tracks refs #28378
• src/hg/makeDb/trackDb/human/hg38/t2tChain.html
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    7a369ff78e7a5a8556095bdb0da39ecd641e43d9 Thu Nov 18 00:34:57 2021 -0800
    data access section for t2t docs page, refs #28380
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
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    6c3ede6cab2516805d69b23c73195b7cdd5b30ea Tue Nov 16 11:57:45 2021 -0800
    Removing release tags from single-cell tracks refs #28378
• src/hg/makeDb/trackDb/human/trackDb.ra
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    754e533ae2a773365fbd26d1db114d079659a001 Thu Nov 18 14:26:09 2021 -0800
    Last edits before announcing orphadata refs #14319
• src/hg/near/LICENSE
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    e13d75a6e72d627977de49db254580c701485b1c Wed Nov 17 06:15:47 2021 -0800
    cleaning up the license situation a little more, refs #27614
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    9bc58644c73868bd9227c6f021801d008a970200 Fri Nov 19 03:03:23 2021 -0800
    fixing all the small LICENSE files that flag protected directories, refs #27614
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    927e0aa76504344d57b1c165207d0527a88855c6 Fri Nov 19 03:32:12 2021 -0800
    Hopefully the last round of fixes to the little license files, refs #27614
• src/hg/utils/automation/doCpgIslands.pl
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    936a6490897222bffd01a9117c6ea9bd9c8cd41a Wed Nov 17 10:22:28 2021 -0800
    eliminate cluster runs use simple command on whole sequence refs #28401
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    2c8115414f9f247308f4d43fe71d2ff92b156c15 Wed Nov 17 10:31:46 2021 -0800
    correct name on bash script refs #28401
• src/hg/utils/automation/doWindowMasker.pl
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    59c1dfd73900ee12b22b5564fa14f28aa19d4807 Wed Nov 17 09:46:45 2021 -0800
    eliminate obsolete commented out code refs #28477
• src/hg/utils/hubCheck/hubCheck.c
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    f90dad3fd12f2d38f0407507297343d692a56a48 Fri Nov 19 14:42:03 2021 -0800
    Adding log setting to httpsCertCheck and making it the new default. This makes it even softer on users, gives us more time to prepare, only logs certs to stderr and only if run as a CGI so that SCRIPT_NAME env var is set. The user does not see anything diffent in behavior and output for log level, but we see cert issues in the log.
• src/hg/utils/otto/grcIncident/runUpdate.sh
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    30e9677ddc4349e1f54dec3d406d7c229502c2ae Tue Nov 16 16:09:06 2021 -0800
    Fixing up discrepancies between hive and tree for otto, refs #28331
• src/hg/utils/otto/mastermind/hg19/chromAlias.tab
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    30e9677ddc4349e1f54dec3d406d7c229502c2ae Tue Nov 16 16:09:06 2021 -0800
    Fixing up discrepancies between hive and tree for otto, refs #28331
• src/hg/utils/otto/mastermind/hg38/chromAlias.tab
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    30e9677ddc4349e1f54dec3d406d7c229502c2ae Tue Nov 16 16:09:06 2021 -0800
    Fixing up discrepancies between hive and tree for otto, refs #28331
• src/hg/utils/otto/nextstrainNcov/nextstrain.py
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    31fcce743b506baaad63423b3f126064a2b0dc56 Fri Nov 12 13:57:59 2021 -0800
    Update to latest clade coloring & names.
• src/hg/utils/otto/omim/bigifyOmim.sh
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    30e9677ddc4349e1f54dec3d406d7c229502c2ae Tue Nov 16 16:09:06 2021 -0800
    Fixing up discrepancies between hive and tree for otto, refs #28331
• src/hg/utils/otto/orphanet/orphanetWrapper.sh
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    9619ee26dc020038db1699585d177f67484e087d Tue Nov 16 13:54:27 2021 -0800
    Add orphanet crontab line and make Lou the victim, refs #14319
• src/hg/utils/otto/otto.crontab
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    9619ee26dc020038db1699585d177f67484e087d Tue Nov 16 13:54:27 2021 -0800
    Add orphanet crontab line and make Lou the victim, refs #14319
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    a563fe5a5b2f61abbdbcc3ecf98fb7686c0d0019 Fri Nov 19 17:39:18 2021 -0800
    Reorganizing otto and officially transferring it to otto user, refs #28331
• src/hg/utils/otto/sarscov2phylo/getNcbi.sh
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    22e94ffbe044de3b15c736105afa2260196e752b Fri Nov 12 13:59:18 2021 -0800
    biosample.jsonl from NCBI Datasets is stable & complete -- finally I can get rid of the redundant EUtils fetching of BioSample.
• src/hg/utils/otto/sarscov2phylo/pango.clade-mutations.tsv
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    7787c0ece98e4377fef9ef76f6873d954d8d7ea8 Fri Nov 12 13:34:42 2021 -0800
    Added lineage B.1.640 (pango-designation release v1.2.94).
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    1d2159abdf40a691de6d3d789781e44b7b3dd167 Fri Nov 12 14:01:19 2021 -0800
    Mask site 28271 in AY lineages because it's deleted (but inconsistently detected) in Delta.
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    40c5f81c53408b270b7b5d991f50b9f7df0ad3b3 Mon Nov 15 09:26:38 2021 -0800
    Cleanup: Remove G24410N (now masked because it's in Problematic Sites). Remove sites masked in maskDelta.sh from AY.* lineages.
• src/hg/utils/otto/uniprot/bed12UniProtFullSeqBgp.as
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    30e9677ddc4349e1f54dec3d406d7c229502c2ae Tue Nov 16 16:09:06 2021 -0800
    Fixing up discrepancies between hive and tree for otto, refs #28331
• src/hg/visiGene/LICENSE
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    e13d75a6e72d627977de49db254580c701485b1c Wed Nov 17 06:15:47 2021 -0800
    cleaning up the license situation a little more, refs #27614
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    9bc58644c73868bd9227c6f021801d008a970200 Fri Nov 19 03:03:23 2021 -0800
    fixing all the small LICENSE files that flag protected directories, refs #27614
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    927e0aa76504344d57b1c165207d0527a88855c6 Fri Nov 19 03:32:12 2021 -0800
    Hopefully the last round of fixes to the little license files, refs #27614
• src/inc/net.h
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    6dd4b07138eb8f479cc4205036c9d6a1794a9f80 Mon Nov 15 13:30:07 2021 -0800
    Add domain exceptions whitelist for allowing us to configure a small number of exceptions that are old servers that are still incompatible with openssl. hg.conf setting httpsCertCheckDomainExceptions or env var https_cert_check_domain_exceptions. This setting is not intended to be used for new servers which should just be advised on correct openssl compatibility, which usually means getting their server to output their intermediate certs as well, or even the cert chain which is typically just 3 certs. refs #28458
• src/jkOwnLib/LICENSE
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    93e587629d6d213790e1ddb9650c1a593cb4902d Fri Nov 19 03:24:06 2021 -0800
    fixing up blat and top level license files a bit more, refs #27614
• src/lib/https.c
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    6dd4b07138eb8f479cc4205036c9d6a1794a9f80 Mon Nov 15 13:30:07 2021 -0800
    Add domain exceptions whitelist for allowing us to configure a small number of exceptions that are old servers that are still incompatible with openssl. hg.conf setting httpsCertCheckDomainExceptions or env var https_cert_check_domain_exceptions. This setting is not intended to be used for new servers which should just be advised on correct openssl compatibility, which usually means getting their server to output their intermediate certs as well, or even the cert chain which is typically just 3 certs. refs #28458
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    f90dad3fd12f2d38f0407507297343d692a56a48 Fri Nov 19 14:42:03 2021 -0800
    Adding log setting to httpsCertCheck and making it the new default. This makes it even softer on users, gives us more time to prepare, only logs certs to stderr and only if run as a CGI so that SCRIPT_NAME env var is set. The user does not see anything diffent in behavior and output for log level, but we see cert issues in the log.
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    5018192830765549851ab9fda888f4714d126029 Sun Nov 21 15:22:05 2021 -0800
    Added 62 domains with cert issues to https.c domain exceptions whitelist. Also adding a special flag value httpsCertCheckDomainExceptions=noHardwiredExceptions which if present in the hg.conf exceptions list causes the hardwired whitelist in https.c to be ignored. Meanwhile other values in the hg.conf softwired list can be still used. This is very handy for testing purposes. refs #28458
• src/lib/net.c
  • lines changed 1, context: html, text, full: html, text
    6dd4b07138eb8f479cc4205036c9d6a1794a9f80 Mon Nov 15 13:30:07 2021 -0800
    Add domain exceptions whitelist for allowing us to configure a small number of exceptions that are old servers that are still incompatible with openssl. hg.conf setting httpsCertCheckDomainExceptions or env var https_cert_check_domain_exceptions. This setting is not intended to be used for new servers which should just be advised on correct openssl compatibility, which usually means getting their server to output their intermediate certs as well, or even the cert chain which is typically just 3 certs. refs #28458
• src/product/ex.hg.conf
  • lines changed 2, context: html, text, full: html, text
    6dd4b07138eb8f479cc4205036c9d6a1794a9f80 Mon Nov 15 13:30:07 2021 -0800
    Add domain exceptions whitelist for allowing us to configure a small number of exceptions that are old servers that are still incompatible with openssl. hg.conf setting httpsCertCheckDomainExceptions or env var https_cert_check_domain_exceptions. This setting is not intended to be used for new servers which should just be advised on correct openssl compatibility, which usually means getting their server to output their intermediate certs as well, or even the cert chain which is typically just 3 certs. refs #28458
  • lines changed 2, context: html, text, full: html, text
    f90dad3fd12f2d38f0407507297343d692a56a48 Fri Nov 19 14:42:03 2021 -0800
    Adding log setting to httpsCertCheck and making it the new default. This makes it even softer on users, gives us more time to prepare, only logs certs to stderr and only if run as a CGI so that SCRIPT_NAME env var is set. The user does not see anything diffent in behavior and output for log level, but we see cert issues in the log.
• src/product/mirrorManual.txt
  • lines changed 3, context: html, text, full: html, text
    6dd4b07138eb8f479cc4205036c9d6a1794a9f80 Mon Nov 15 13:30:07 2021 -0800
    Add domain exceptions whitelist for allowing us to configure a small number of exceptions that are old servers that are still incompatible with openssl. hg.conf setting httpsCertCheckDomainExceptions or env var https_cert_check_domain_exceptions. This setting is not intended to be used for new servers which should just be advised on correct openssl compatibility, which usually means getting their server to output their intermediate certs as well, or even the cert chain which is typically just 3 certs. refs #28458
  • lines changed 3, context: html, text, full: html, text
    f90dad3fd12f2d38f0407507297343d692a56a48 Fri Nov 19 14:42:03 2021 -0800
    Adding log setting to httpsCertCheck and making it the new default. This makes it even softer on users, gives us more time to prepare, only logs certs to stderr and only if run as a CGI so that SCRIPT_NAME env var is set. The user does not see anything diffent in behavior and output for log level, but we see cert issues in the log.
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 2, context: html, text, full: html, text
    a0fa86a679197c86d844b92ee3a5de6ee511f91a Mon Nov 22 10:31:10 2021 -0800
    v424 preview2, refs #28521

• lines changed: 2507
• files changed: 183