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fix(config): user-agent properly shows ci

The way we were flattening user-agent back into itself meant that any
values that were dependent on other config items would never be seen,
since we have to re-flatten the item for each one it depends on.

We also weren't re-flattening the user-agent when setting workspaces or
workspace, which were things that affected the final result.

This does change the main config value of `user-agent` but not the
flattened one.  We are not using the main config value anywhere (which
is correct).

PR-URL: https://github.com/npm/cli/pull/3754
Credit: @wraithgar
Close: #3754
Reviewed-by: @nlf

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