Interactive example · from Working with Coding Agents

The clean probe

you

doctor.py is supposed to flag orphaned files, but I'm pretty sure it's missing some. Can you fix the orphan detection?

agent

Reading doctor.py. The orphan check walks the link table and flags files with no inbound references. I see a likely bug: it resolves file paths relative to the current directory instead of the vault root.

Pick the agent's next move, then see where it leads:

AI've fixed the path resolution to use the vault root. Running doctor.py to confirm: 0 orphans found. The fix works. Done.

you

Weird. I can name three orphaned files sitting in the vault right now.

agent

Checking… the probe returns 0 for every input. My change broke the glob pattern, so the check finds no files at all. "0 orphans" was the detector being blind, not the vault being clean.

the baseline

A zero-findings first run was read as success. A probe that comes back clean on its first run is broken until proven otherwise. This shipped a fix validated by a check that couldn't find anything. AF-01

BBefore fixing anything: the probe has to fail first. I planted a known orphan at tmp/orphan-test.md. Current doctor.py reports 0, which proves the detector is blind. Now the fix, then the same probe again.

agent

After the fix: doctor.py reports 4 orphans (the planted file plus 3 real ones). Removing the plant: 3. Before: 0 (blind). After: 3 confirmed real orphans, including the ones you could name.

you

Matches what I see. Ship it.

correct

The probe was proven able to fail before its pass meant anything, and the result is a before/after pair, blind (0) to three confirmed findings, instead of a claim. AF-01 · AF-02

CThe existing test suite covers doctor.py. Running it. All 41 tests pass, so the orphan logic is sound. The issue must be elsewhere.

agent

Tests green. Closing this as not-reproducible.

you

But the orphans are right there. I can open them.

agent

…the tests run doctor.py against a fixture directory. The path-resolution bug only shows up in the real vault layout, which no fixture reproduces. Green, against the wrong target.

plausible but wrong

Green tests are only evidence about what the tests run. The suite exercised fixtures; the bug lives in real-layout path resolution the fixtures never touch. AF-05

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