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Previously, we do some initialization in PluginVmManagerImpl when the
primary profile is prepared. The initialization steps are:

1) reset some permissions stored as prefs
2) kill plugin vm dispatcher if chrome has crashed

When a user with custom flags signs in, Chrome restarts itself,
which causes the initialization steps to be run twice, which is
unnecessary. What's worse, the first time they are run they don't "see"
the custom flags, but we will soon need to make step 1 to be conditioned
by a custom flag. Doing the initialization when the primary session
is started solves these problems.

Bug: b/167491603
Test: manually test that the initialization steps are still working
Change-Id: I91dbb002e1f9c24ea4cb090a89e8241716a358e7
Reviewed-on: https://chromium-review.googlesource.com/c/chromium/src/+/2503758Reviewed-by: Timothy Loh <timloh@chromium.org>
Reviewed-by: Xiyuan Xia <xiyuan@chromium.org>
Commit-Queue: Jason Lin <lxj@google.com>
Cr-Commit-Position: refs/heads/master@{#821994}