sim: run: move linking into top-level

Automake will run each subdir individually before moving on to the next
one.  This means that the linking phase, a single threaded process, will
not run in parallel with anything else.  When we have to link ~32 ports,
that's 32 link steps that don't take advantage of parallel systems.  On
my really old 4-core system, this cuts a multi-target build from ~60 sec
to ~30 sec.  We eventually want to move all compile+link steps to this
common dir anyways, so might as well move linking now for a nice speedup.

We use noinst_PROGRAMS instead of bin_PROGRAMS because we're taking care
of the install ourselves rather than letting automake process it.

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