timer_wrap: Timer.now always update loop time

In `Timer.now` always update the loop time by calling uv_update_time.
Previously we were trying to cache the loop time to prevent extra
syscalls. While a noble goal, it can cause timers to fire early in
certain circumstances. Especially seen in cpu bound work loads or work
loads with synchronous file operations.
pipe_wrap: squelch integer type conversion warning
vm: update API to use options argument

Passing a filename is still supported in place of certain options
arguments, for backward-compatibility, but timeout and display-errors
are not translated since those were undocumented.

Also managed to eliminate an extra stack trace line by not calling
through the `createScript` export.

Added a few message tests to show how `displayErrors` works.
vm: document vm2's changes.

- The caveats no longer apply.
- Document options arguments, including `displayErrors` and the
  different things it means in each place.
- Re-did examples to be more on point, e.g. `runInContext` example
  runs multiple scripts in the same context.
- Documented how `vm.createContext`s meaning has substantially changed,
  and is now more of a "contextifier" than a "creator."
- Reordered vm functions to be readable in order; the concept of
  contextifying needs to come before `runInContext` and
  `runInNewContext`.
- Documented new `vm.isContext`.
- Documented the `vm.Script` constructor, instead of `createScript`,
  since factory methods are silly and we wanted to document the class's
  methods anyway.
- Documented `script.runInContext`.
- Change stability to stable, if I may be so bold.
crypto: make error buffer non-static

Doesn't matter now but it will if/when we have support for multiple
threads.
crypto: remove misleading comment
crypto: make root_cert_store variable extern

Before this commit it was declared static (in a header file!), meaning
it got duplicated in every file that includes it.

A few duplicated pointers is not the end of the world but it introduces
a lot of potential for confusion because root_cert_store in file A is
not the root_cert_store in file B.

Moral of the story: don't declare static variables in header files.
crypto: remove NodeBIO::GetMethod()

Remove NodeBIO::GetMethod() and replace calls to BIO_new() with calls
to the new NodeBIO::New() function.

This commit basically reshuffles some code in order to make it explicit
that the NodeBIO BIO_METHOD is const.
src: remove unused Persistent<FunctionTemplate>
uv: upgrade to v0.11.11