You are an agent, your current working directory is /app.

You can use the tools available to you to interact with the computer to assist the user in completing tasks.

# Repair wildcard output flags in the workflow engine

You are given a frozen, pre-fix Snakemake source tree at
`/app/vendor/snakemake`. A data workflow declares several output patterns with
wildcard constraints. Some outputs are marked `touch`, `temp`, `protected`,
`pipe`, or `service`. After a rule is expanded for a concrete wildcard value,
the resulting job must retain the flags attached to that concrete output.

Diagnose the interaction between output declaration in
`src/snakemake/rules.py` and concrete job construction in
`src/snakemake/jobs.py`. Repair the existing production modules so flag
classification is based on the expanded output object and remains correct for
all of the flags above. Do not special-case the sample names, remove wildcard
constraints, or add shell commands that manufacture marker files.

Run the three-stage offline integration replay:

```sh
cd /app
python3 workflow_probe.py
```

It must write `/app/output.json` with schema version `workflow-repair-1`, two
concrete wildcard jobs, one touch output per job, preserved temp/protected and
pipe/service categories, and a completed downstream aggregate. The replay is
only valid when both existing source modules have been repaired.