Enumerate an array, grouping duplicates

Dyalog APL, 5 bytes

(⊂,)⌸

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,⌸ for 2 bytes almost works, but has trailing zeroes :/

J, 12 bytes

~.,&.><@I.@=

Zero-indexed.

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If you can remove all of the work I'm doing with boxes, you can probably reduce the bytecount by quite a bit. I'm going to see if I can figure that out.

Explanation

This is probably too early to be explaining (there ought to be more golfs).

~. ,&.> <@I.@=
             =  Self-classify (comparison of each unique element to array)
            @   Composed with
          I.    Indices of ones (where it's equal)
         @      Composed with
        <       Boxed (how we deal with arrays of unequal length)
   ,&.>         Joined with
      >          Unbox each
   ,             Concatenate
    &.           Box again
~.              Unique elements

05AB1E, 10 bytes

ÙεDIQƶ0K)˜

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Explanation

Ù             # remove duplicates
 ε            # apply to each element
  D           # duplicate
   IQ         # compare for equality with input
     ƶ        # multiply each element by its index (1-based)
      0K      # remove zeroes
        )˜    # wrap in a flattened list