Let say that you want to build for Java 8 and errorprone checks off but keep the tools directory provided with Bazel in the package path, you could do that by having the following rc file:

build --javacopt="-extra_checks:off"
build --javacopt="-source 8"
build --javacopt="-target 8"

However, the file would becomes quickly overloaded, especially if you take all languages and options into account. Instead, you can tweak the java_toolchain rule that specifies the various options for the java compiler. So in a BUILD file:

java_toolchain(
    name = "my_toolchain",
    encoding = "UTF-8",
    source_version = "8",
    target_version = "8",
    misc = [
        "-extra_checks:on",
    ],
)

And to keep it out of the tools directory (or you need to copy the rest of the package), you can redirect the default one in a bazelrc:

build --java_toolchain=//package:my_toolchain

In the future, toolchain rules should be the configuration points for all the languages but it is a long road. We also want to make it easier to rebind the toolchain using the bind rule in the WORKSPACE file.