sim: mcuboot-sys: Avoid duplicate C files

When building mcuboot-sys, the build script currently adds some
duplicate files.  When used as a library, this works, because the code
is linked in as a library.  However, when mcuboot-sys is tested itself,
all specified files will be brought in, which results in duplicate
symbols for these files.

Fix this by keeping track of all of the files that we've added, and
making sure to add each file once.  Additionally, instead of using the
orphaned files in mbedtls-asn1, just always use the verions in the main
mbedtls library.  There are some configurations of the code that end up
using both the extracted files and the full mbed TLS.  Avoid that
conflict by just always using the full tree.

Signed-off-by: David Brown <david.brown@linaro.org>