Description of the bug:

When Bzlmod is enabled, //src/test/shell/integration:configured_query_test fails with

** test_config_function ********************************************************
-- Test log: -----------------------------------------------------------
$TEST_TMPDIR defined: output root default is '/b/f/w/_tmp/7db115b6dfb285ceb10442ec6acaf9d3' and max_idle_secs default is '15'.
Computing main repo mapping: 
Loading: 
Loading: 0 packages loaded
Analyzing: target //test_config_function:tool (0 packages loaded, 0 targets configured)
INFO: Analyzed target //test_config_function:tool (0 packages loaded, 1 target configured).
INFO: Found 1 target...
ERROR: Error doing post analysis query: Evaluation failed: No target (in) //test_config_function:tool could be found in the configuration with checksum '50265a7'
INFO: Elapsed time: 0.333s, Critical Path: 0.00s
INFO: 0 processes.
ERROR: Build did NOT complete successfully

see #19785 (comment)

Which category does this issue belong to?

Configurability

What's the simplest, easiest way to reproduce this bug? Please provide a minimal example if possible.

To reproduce:

• Remove disable_bzlmod from src/test/shell/integration/configured_query_test.sh
• bazel test //src/test/shell/integration:configured_query_test --test_filter test_config_function

Which operating system are you running Bazel on?

No response

What is the output of bazel info release?

No response

If bazel info release returns development version or (@non-git), tell us how you built Bazel.

No response

What's the output of git remote get-url origin; git rev-parse master; git rev-parse HEAD ?

No response

Is this a regression? If yes, please try to identify the Bazel commit where the bug was introduced.

No response

Have you found anything relevant by searching the web?

No response

Any other information, logs, or outputs that you want to share?

It's very likely //src/test/java/com/google/devtools/build/lib/runtime:ConfigCommandTest is failing with the same reason when enabling Bzlmod.