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This repository minimally reproduces an error I'm seeing with bazel --incompatible_remap_main_repo in Bazel 0.24.0rc2:

$ bazel --incompatible_remap_main_repo :x_library
Loading: 
Loading: 0 packages loaded
INFO: Build option --toolchain_resolution_debug has changed, discarding analysis cache.
Analyzing: target //:x_library (0 packages loaded, 0 targets configured)
ERROR: While resolving toolchains for target //:x_library: no matching toolchains found for types @io_bazel_rules_x//:x_toolchain_type
ERROR: Analysis of target '//:x_library' failed; build aborted: no matching toolchains found for types @io_bazel_rules_x//:x_toolchain_type
INFO: Elapsed time: 0.098s
INFO: 0 processes.
FAILED: Build did NOT complete successfully (0 packages loaded, 28 targets configured)
FAILED: Build did NOT complete successfully (0 packages loaded, 28 targets configured)

The target //:x_library is an instance of the x_library rule, defined in def.bzl. x_library requires a toolchain of type @io_bazel_rules_x//:x_toolchain_type.

The WORKSPACE for this repository declares an external repo, x_sdk with the build file x_sdk.BUILD.bazel. This build file declares x_toolchain_impl, a x_toolchain target (loaded from @io_bazel_rules_x//:def.bzl) and x_toolchain, a toolchain target for x_toolchain_impl with type @io_bazel_rules_x//:x_toolchain_type. The WORKSPACE for this repository calls register_toolchains("@x_sdk//:x_toolchain").

My expectation is that //:x_library will use the toolchain @x_sdk//:x_toolchain. This seems to work without the flag. When the flag is on, it's as if the toolchain doesn't exist. When --toolchain_resolution_debug is given, it's as if the toolchain doesn't exist.

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