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JAL-3248 Moved old README to doc/old_README and put pointers in new README for deskopt application building and JalviewJS building

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JAL-3248 Archived old README. Added new README to point user to doc/building.md

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JAL-3456 fixed some backticks in README.md

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JAL-3210 JAL-3456 Mothballing work done on using goomph for jalviewjs build

JAL-3210 JAL-3456 Mothballing work done on using goomph for jalviewjs build

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JAL-3210 gradle jalviewjsServer now working. Up to date src and swingjs from Jalview-JS/...applet branch. Transpiles and launches.

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JAL-3210 Improvements to eclipse detection. New src tree and SwingJS updated from the applet branch. AND IT WORKS (sometimes)

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JAL-3210 Now includes creating the .project, .classpath and .settings as a depenedency

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JAL-3210 Barebones gradle/buildship/eclipse. See README

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Merge branch 'feature/JAL-3063JAXB' into Jalview-BH/JAL-3026-JAL-3063-JAXB

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JAL-3065 - amended commit 4906697ab6e5a79fbce3baae89f7f64178c9a739 to exclude .settings/..groovy Added notes to the instructions, also adjusted the jalviewDesktopRunner test to lookup OS and use ';' or ':' accordingly. All the CommandLineOperations tests failed on my (hastily set up) linux box, so I'm committing and will test on MacOS too.

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Added notes to the instructions, also adjusted the jalviewDesktopRunner test to lookup OS and use ';' or ':' accordingly. All the CommandLineOperations tests failed on my (hastily set up) linux box, so I'm committing and will test on MacOS too.

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should really explain what path to classes is as well as path to lib here

should really explain what path to classes is as well as path to lib here

have you checked this works on Windows ? If it doesn't we should provide an alternative commandline

have you checked this works on Windows ? If it doesn't we should provide an alternative commandline

JAL-3065

Change in all repo documentation advising launching Jalview with the

-Djava.ext.dirs=LIB

option to now use

-classpath="LIB/*:..."

instead. Using the -Djava.ext.dirs= option masks the JRE's own ext dir

which contains the sunjce packages. This manifests as cipher problems

when accessing https resources (in particular https://www.ebi.ac.uk/...

when searching for PDB structures, activated when choosing Sequence->"3D

Structure Data...")

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JAL-3026 'dropins' !

JAL-3026 update README with instructions on setting up Eclipse for java2script and running unzip-to-site to update the site directory after a build.

JAL-2069 update spike branch with latest

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JAL-2818 modified README for launching jalview from source build

JAL-1620 version bump and release notes

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added notes on third party library licencing and updated netbeans builder library deps

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Revert "just a test"

This reverts commit 0f56a75191c95a02b5f5ee90d9a6a57f72b0433b.

just a test

Jalview 2.6 source licence

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Note on build target being usage

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Add notes on proxy settings

backslash irrelevant in java

Remove .txt, add command line instruction

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