Cleanup option parsing and config.toml.example

- Add an assertion that `link-shared = true` when `thin-lto = true`.
  Previously, link-shared would be silently overwritten.

- Get rid of `Option<bool>` in bootstrap/config.rs. Set defaults
  immediately instead of delaying until later in bootstrap. This makes
  it easier to find what the default value is.

- Remove redundant `config.x = false` when the default was already false
- Set defaults for `bindir` in `default_opts()` instead of `parse()`
- Update `download-ci-llvm = if-supported` option to match bootstrap.py
- Remove redundant check for link_shared. Previously, it was checked twice.

- Update various options in config.toml.example to their defaults.
  Previously, some options showed an example value instead of the
  default value.

- Fix incorrect defaults in config.toml.example
  + `use-libcxx` defaults to false
  + Add missing `check-stage = 0`
  + Update several defaults to be conditional (e.g. `if incremental { 10 } else { 100 }`)

- Remove redundant defaults in prose
- Use the same comment for the default and target-dependent `musl-root`
- Fix typos
- Link to `cc_detect` for `cc` and `cxx`, since the logic is ... complicated.
- Update more defaults to better reflect how they actually get set
- Remove ignored `gpg-password-file` option

  This stopped being used in
  https://github.com/rust-lang/rust/commit/7704d35accfe1b587ce41ea09ca3bf6a47aca117,
  but was never removed from config.toml.

- Remove unused flags from `config.toml`
    + Disallow `infodir` and `localstatedir` in `config.toml`
    + Allow the flags in `./configure`, but give a warning that they will be
      ignored.
    + Fix incorrect comment that `datadir` will be ignored.

    Example output:

    ```
    $ ./configure --set install.infodir=xxx
    configure: processing command line
    configure:
    configure: install.infodir      := xxx
    configure: build.configure-args := ['--set', 'install.infodir=xxx']
    warning: infodir will be ignored
    configure:
    configure: writing `config.toml` in current directory
    configure:
    configure: run `python /home/joshua/rustc3/x.py --help`
    configure:
    ```

- Update CHANGELOG
- Add "as an example" where appropriate
- Link to an issue instead of to ephemeral chats

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