Detect if there are unlinked version stubs under `bin/` and fail if they are present

Sometimes the users get their `bin/` stubs in inconsistent state, where there are unlinked `bin/.-.pkg` files.

We should detect if this is the case, and either fail or show a warning to the user so they can clean them away.

Start by tracing Hermit's handling of version stubs under the bin/ directory, focusing on how it identifies linked and unlinked bin/-.pkg files. Done means inconsistent unlinked stubs are detected and the user either receives a warning or the operation fails, with the chosen behavior verified against the issue's scenario.

Written by the indexing model from the issue text.