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We can see that the support for JavaScript on home page components is being phased out as described here:

http://docs.releasenotes.salesforce.com/en-gb/summer14/release-notes/rn_forcecom_home_page_components.htm

Is there an alternative to add java script on a homepage?

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It really depends on what you are going to do:

Use Case 1

If you just need a homepage component which uses JavaScript and have the access of JavaScript limited to the component itself then you should use the new HTML Area Home Page Components: http://docs.releasenotes.salesforce.com/en-gb/summer14/release-notes/rn_forcecom_home_page_components.htm

Use Case 2

If you need your JavaScript to access the entire homepage and/or other pages where the sidebar is available, you can have a look at the workaround described here End of javascript sidebar workarounds? which is working at least in summer'14. This would apply mostly to use cases discussed here Why do we still need to hack the Sidebar? Usecases - Workarounds - Alternatives please mind, that these approaches may also be discontinued at some point in the future by Salesforce.

1

I think you should be able to create a visualforce component and put your Javascript in there instead.

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