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Repository reorg
Ryan Guild preferred excessively elaborate file hierarchies. Since he has abandoned the project we're going to go with what makes sense to me (and is arguably more correct - 3dmol is the only true package, so why factor it into a packages directory). Clean up some other issues with typescript and imports.
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## Feature Request
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1. Please go through the 3Dmol.js [js documentation](http://3dmol.csb.pitt.edu/packages/3Dmol/doc/index.html) and [ts documentation](http://3dmol.csb.pitt.edu/packages/3Dmol/doc/typescript/index.html) to check whether the feature is already present.
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1. Please go through the 3Dmol.js [js documentation](http://3dmol.org/doc/index.html) and [ts documentation](http://3dmol.org/doc/typescript/index.html) to check whether the feature is already present.
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2. Ensure that the feature request is new and is not already proposed.
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3. If the feature request is new, follow the feature request template to submit an issue.
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