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Download the new TinyMCE tarball and extract it to your Desktop (or other easily accessible location)
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Delete the copy of TinyMCE in the plugin at lib/tiny_mce/assets/tiny_mce (this ensures old/removed files are deleted)
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Copy the source files of TinyMCE (not the documentation) to lib/tiny_mce/assets/tiny_mce (so in that folder you should have a tiny_mce.js file)
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Update CHANGELOG_TINYMCE (simply download and overwrite the contents with that of tinymce.moxiecode.com/js/tinymce/changelog.txt)
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Update lib/tiny_mce/valid_tinymce_options.yml with any new options, or remove old ones, as described in the tinymce changelog
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Download all ‘Complete’ locales from tinymce.moxiecode.com/i18n/index.php?ctrl=lang&, unpack, and copy into place
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Update lib/tiny_mce/valid_tinymce_langs.yml with any new languages, or remove old/incomplete ones
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Update the CHANGELOG_PLUGIN.rdoc to say what you upgraded from, what you upgraded to, and your name
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Update the ‘Bundled TinyMCE version’ value at the bottom of README.rdoc
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Commit, push, and send pull request to github.com/kete/tiny_mce