Add safe guards for relative paths

This commit adds multiple safe guards for relative paths, ensuring they
never traverse outside the working directory.

The `SafeRelativePath` flag calculates the safe relative path based on a
relative base dir, which results in a flattened path.

The write methods of `manifestgen` make use of the `SecureJoin` as well,
to ensure writes are never outside of the given directory when used as
a lib outside of the CLI.

Signed-off-by: Hidde Beydals <hello@hidde.co>