I want to create a plugin and I need to override some calendar javascript files (calendar.js and calendar.setup.js)
Can I add these files to plugin web resources (atlassian-plugin.xml) ? on the other hand I want to load these javascript files instead of JIRA core web resources. any help would be greatly appreciated.
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As I know, plugin resources are loaded after JIRA resources (moreover you can enforce this using <dependency> tag for your resources to depend upon JIRA resource that serves calendar.js and calendar.setup.js).
calendar.js and calendar.setup.js define some global variables and your script which will be loaded after JIRA's calendar versions should override these global vars so your custom script will be used. Just make sure to load your scripts into appropriate context. Look here for more details.
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