sim: document.

This commit includes additional non-documentation changes, related to
issues found while documenting it:
- `Simulator.run_until()` no longer accepts a `run_passive=` argument.
  Passive no longer exist and in any case defaulting to `False` does not
  make a lot of sense from an API perspective.
- `add_clock()`'s `phase=` argument, when specified, no longer has
  `period/2` added to it. This wasn't the documented behavior in first
  place and it makes no sense to do that.
- `add_clock()` raises a `NameError` if a clock domain does not exist,
  instead of `ValueError`.
- `add_clock()` raises a `DriverConflict` if a clock domain is already
  being driven by a clock, instead of `ValueError`.
- GTKWave is no longer a part of the installation instructions, and both
  Surfer and GTKWave are recommended (in this order).

docs/stdlib/memory.rst

@@ -171,21 +171,35 @@ However, the memory read port is also configured to be *transparent* relative to
 
 
 Simulation
-==========
+++++++++++
 
-.. todo::
+There are two ways to interact with a memory array in a simulator: requesting a read and/or write port that is used only in a testbench, or directly reading and writing memory contents. In most cases, directly accessing memory contents using :meth:`MemoryData.__getitem__ <amaranth.hdl.MemoryData.__getitem__>` is more convenient.
 
-    This section will be written once the simulator itself is documented.
+For example, this :doc:`testbench </simulator>` will clear the least significant bit of every memory row:
+
+.. testcode::
+
+    async def testbench(ctx):
+        for index in len(memory.data):
+            ctx.set(memory.data[index], ctx.get(memory.data[index]) & ~1)
 
 
 Memory description
 ==================
 
 .. autoexception:: amaranth.hdl.AlreadyElaborated
-   :noindex:
+    :noindex:
+
+    ..
+        :canonical: amaranth.hdl.AlreadyElaborated
+        (not available until `amaranth.hdl` documents it)
 
 .. autoclass:: amaranth.hdl.MemoryData
 
+    ..
+        :canonical: amaranth.hdl.MemoryData
+        (not available until `amaranth.hdl` documents it)
+
 
 Memory component
 ================