bootstrap: Fix running multiple times in-source

Since commit v3.9.0-rc1~281^2 (Use quotes for non-system includes,
2017-04-11) we include `cmConfigure.h` via `""` instead of `<>`.
This breaks the `bootstrap` script when run more than once in an
in-source build.  In that case `cmConfigure.h` is generated next
to the source files that include it, so `""`-style includes prevent the
`Bootstrap.cmk/cmConfigure.h` file from being included during bootstrap.

Fix this by teaching the bootstrap script to remove any `cmConfigure.h`
that may have been generated by an earlier run in an in-source build.

Fixes: #17082