I got it to work and wrote my process up 
here: https://github.com/JuliaLang/julia/issues/10766

On Monday, September 21, 2015 at 9:05:38 PM UTC-7, Amit Murthy wrote:
>
> julia> Pkg.publish()
>
> INFO: Validating METADATA
> INFO: Pushing LibCURL permanent tags: v0.1.6
> INFO: Submitting METADATA changes
> INFO: Forking JuliaLang/METADATA.jl to amitmurthy
> INFO: Recompiling stale cache file /home/amitm/.julia/lib/v0.4/JSON.ji for 
> module JSON.
> Enter host password for user 'amitmurthy':
> INFO: Two-factor authentication in use.  Enter auth code.  (You may have 
> to re-enter your password.)
> Authentication code: xxxxxx
> Enter host password for user 'amitmurthy':
> INFO: Retrieving existing GitHub token. (You may have to re-enter your 
> password twice more.)
> Enter host password for user 'amitmurthy':
> New authentication code: xxxxxx
> Enter host password for user 'amitmurthy':
> INFO: Could not authenticate with existing token. Deleting token and 
> trying again.
> Enter host password for user 'amitmurthy':
> INFO: Two-factor authentication in use.  Enter auth code.  (You may have 
> to re-enter your password.)
> Authentication code: xxxxxx
> Enter host password for user 'amitmurthy':
> INFO: Retrieving existing GitHub token. (You may have to re-enter your 
> password twice more.)
> Enter host password for user 'amitmurthy':
> New authentication code: xxxxxx
> Enter host password for user 'amitmurthy':
> ERROR: forking JuliaLang/METADATA.jl failed: Bad credentials
>  in error at ./error.jl:21
>  in fork at pkg/github.jl:144
>  in pull_request at pkg/entry.jl:327
>  in publish at pkg/entry.jl:394
>  in anonymous at pkg/dir.jl:31
>  in cd at file.jl:22
>  in cd at pkg/dir.jl:31
>  in publish at pkg.jl:61
>
>
>
> After entering credentials umpteen number of times, it just barfs out. Any 
> pointers?
>
>
>
>
>

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