Clean and update some update-related file and comments.

MSFragger-GUI/src/com/dmtavt/fragpipe/Bundle.properties

@@ -178,19 +178,5 @@ philosopher.version.latest-compatible.4.5=20180302
 
 philosopher.download.url=https://api.github.com/repos/Nesvilab/philosopher/releases/latest
 
-# the below link is copid from browser and IS WRONG, use https://raw.githubusercontent.com/user/repo/branch/path-to-file insteam
-#update-package.workflows-01.ver[13.0,]=https://github.com/chhh/FragPipe/raw/updates/MSFragger-GUI/updates/LFQ-update-1.zip
-#update-package.workflows-01.ver[13.0,].desc=update-1: New workflow
-
-# here's the correct link
-#update-package.workflows-02.ver[13.0,]=https://raw.githubusercontent.com/chhh/FragPipe/updates/MSFragger-GUI/updates/LFQ-update-1.zip
-#update-package.workflows-03.ver[13.0,].desc=update-2: New workflow
-
-#update-package.workflows-03.ver[13.0-RC2,]=https://raw.githubusercontent.com/chhh/FragPipe/updates/MSFragger-GUI/updates/update-test-01.zip
-#update-package.workflows-03.ver[13.0-RC2,].desc=Update service test 1: New workflow delivered through an update, from dev repo
-#
-#update-package.workflows-04.ver[13.0-RC2,]=https://raw.githubusercontent.com/Nesvilab/FragPipe/updates/MSFragger-GUI/updates/update-test-02.zip
-#update-package.workflows-04.ver[13.0-RC2,].desc=Update service test 2: Another workflow delivered through an update, from main repo
-
-#update-package.workflows-05.ver[13.0-RC10,]=https://raw.githubusercontent.com/Nesvilab/FragPipe/updates/MSFragger-GUI/updates/workflows-2020-06-05.zip
-#update-package.workflows-05.ver[13.0-RC10,].desc=Update: new workflows from Alexey
+#update-package.tmt-integrator-update-2023-12-20.ver[21.0,21.0]=https://raw.githubusercontent.com/Nesvilab/FragPipe/updates/MSFragger-GUI/updates/tmt-integrator-update-2023-12-20.zip
+#update-package.tmt-integrator-update-2023-12-20.ver[21.0,21.0].desc=Fix a bug in TMT-Integrator that in the single/multi-site reports, the site, protein start, and protein end are off by one.

MSFragger-GUI/src/umich/msfragger/gui/Bundle.properties

@@ -178,19 +178,5 @@ philosopher.version.latest-compatible.4.5=20180302
 
 philosopher.download.url=https://api.github.com/repos/Nesvilab/philosopher/releases/latest
 
-# the below link is copid from browser and IS WRONG, use https://raw.githubusercontent.com/user/repo/branch/path-to-file insteam
-#update-package.workflows-01.ver[13.0,]=https://github.com/chhh/FragPipe/raw/updates/MSFragger-GUI/updates/LFQ-update-1.zip
-#update-package.workflows-01.ver[13.0,].desc=update-1: New workflow
-
-# here's the correct link
-#update-package.workflows-02.ver[13.0,]=https://raw.githubusercontent.com/chhh/FragPipe/updates/MSFragger-GUI/updates/LFQ-update-1.zip
-#update-package.workflows-03.ver[13.0,].desc=update-2: New workflow
-
-#update-package.workflows-03.ver[13.0-RC2,]=https://raw.githubusercontent.com/chhh/FragPipe/updates/MSFragger-GUI/updates/update-test-01.zip
-#update-package.workflows-03.ver[13.0-RC2,].desc=Update service test 1: New workflow delivered through an update, from dev repo
-#
-#update-package.workflows-04.ver[13.0-RC2,]=https://raw.githubusercontent.com/Nesvilab/FragPipe/updates/MSFragger-GUI/updates/update-test-02.zip
-#update-package.workflows-04.ver[13.0-RC2,].desc=Update service test 2: Another workflow delivered through an update, from main repo
-
-#update-package.workflows-05.ver[13.0-RC10,]=https://raw.githubusercontent.com/Nesvilab/FragPipe/updates/MSFragger-GUI/updates/workflows-2020-06-05.zip
-#update-package.workflows-05.ver[13.0-RC10,].desc=Update: new workflows from Alexey
+#update-package.tmt-integrator-update-2023-12-20.ver[21.0,21.0]=https://raw.githubusercontent.com/Nesvilab/FragPipe/updates/MSFragger-GUI/updates/tmt-integrator-update-2023-12-20.zip
+#update-package.tmt-integrator-update-2023-12-20.ver[21.0,21.0].desc=Fix a bug in TMT-Integrator that in the single/multi-site reports, the site, protein start, and protein end are off by one.