fix(doctor): probe ast-grep so bootstrap stops reporting ok on a machine where edit.ast-grep-plan cannot run

[2233admin]

The finding

code-intel doctor bootstrap --repo-path . --no-require-repowise --require-provider-conformance --json returned "ok": true, "missing": [], and a tools array of exactly six entries: rg, git, python, repowise, repomix, sentrux. The probe list is hardcoded in crates/code-intel-cli/src/doctor_bootstrap/mod.rs and contained no ast-grep.

That is a blind spot with three independent confirmations in this tree:

• orchestration/integrations.json ships edit.ast-grep-plan as a capability with runtimeAdapter: edit.ast-grep-plan.compat.
• crates/code-intel-cli/src/structured_edit.rs resolves tool_path::resolve("ast-grep") and shells out to ast-grep --version; a machine without it fails at capability-exec time with AdapterError::Unavailable("start ast-grep: ...").
• .github/workflows/ci.yml installs a sha256-pinned ast-grep 0.42.3 in both jobs and throws on a version mismatch, and orchestration/toolchain-versions.v1.json carries an ast-grep entry with a command probe.

So CI treated ast-grep as a hard dependency while the doctor treated it as nonexistent.

The fix

One probe added to the tools vector, required: false.

Optional is the honest setting, not a softening: orchestration/toolchain-versions.v1.json already declares ast-grep with "required": false, and integrations.json declares edit.ast-grep-plan with "required": false. Making it required would have flipped the doctor red on every installed machine without ast-grep — a gate change, not a bug fix. What changes is that the observation now reports the tool: found plus a resolved source path, and a MISSING ast-grep line in the human rendering when it is absent, instead of silently omitting it.

No existing green turns red, and no gate was weakened, waived, or relabelled.

Tests

Two, both of which fail if the one-line probe is reverted:

1. doctor_bootstrap::tests::observation_carries_the_v1_contract_and_every_retired_check — the existing tool-name-order assertion gains "ast-grep".
2. the_probe_list_covers_the_external_tool_a_shipped_capability_shells_out_to (new, tests/doctor_bootstrap_cli.rs) — reads the shipped orchestration/integrations.json, confirms edit.ast-grep-plan is still a runtime capability, and only then requires the probe list to cover it. The manifest read is the point: retiring the capability relaxes the test instead of leaving a restated constant behind.

Revert proof. With probe::probe_tool("ast-grep", false, prefix) removed and nothing else changed:

test the_probe_list_covers_the_external_tool_a_shipped_capability_shells_out_to ... FAILED
  doctor bootstrap never probes ast-grep: [rg, git, python, repowise, repomix, sentrux]

test doctor_bootstrap::tests::observation_carries_the_v1_contract_and_every_retired_check ... FAILED
  left:  ["rg", "git", "python", "repowise", "repomix", "sentrux"]
  right: ["rg", "git", "python", "repowise", "repomix", "sentrux", "ast-grep"]

Restored, both pass.

Digest re-pin

capabilityDeclaration.implementation.toolchainDigests for the doctor capability pins doctor_bootstrap/mod.rs. Re-pinned by hand (b4b6fc64… -> ef26c267…) and verified with sha256, per the known repin --write blind spot (#133). registry_toolchain_digests_bind_the_adapter_and_dispatch_sources caught the stale pin and now passes.

Verification

• cargo test --workspace --locked — 2959 passed, 51 suites, fully green.
• cargo fmt -p code-intel -- --check — clean.
• Authoritative self-scan (run execute --repo . --manifest orchestration/integrations.json --doctor-require-repowise false) — exit 0, "failures": {"domain": [], "process": []}, all 8 nodes verdict: pass.
• God-file ratchet checked by hand before editing: mod.rs sits at 25 recognised functions, and the rule is functions > 25 && loc > 400. Adding any new fn to that file — including a test fn — would have made it a god file and tripped the ratchet. That is why the new test lives in tests/doctor_bootstrap_cli.rs and the in-file change is a comment plus one expression. Post-change: mod.rs loc 779 / 25 fns, doctor_bootstrap_cli.rs loc 312 / 11 fns — neither trips it.

Post-fix output

{"found": true, "name": "ast-grep", "required": false,
 "source": "...\\Scripts\\ast-grep.exe"}

Seven entries now, and the doctor answers for a tool a shipped capability cannot run without.

Refs the dogfooding finding F4-doctor-blind-to-ast-grep. Do not merge without review.

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[coderabbitai]

📝 Walkthrough

Summary by CodeRabbit

• New Features

  • The diagnostic tool now detects and reports whether the optional ast-grep tool is available.
  • Tool availability is displayed as a clear true/false status in diagnostic results.

• Bug Fixes

  • Updated integration metadata to ensure diagnostics use the correct toolchain configuration.

Walkthrough

The doctor bootstrap now probes ast-grep as an optional tool and reports its availability. Contract and CLI regression tests verify the observation. The doctor integration declaration also uses an updated toolchain digest.

Changes

Doctor bootstrap observation

Layer / File(s)	Summary
Integration toolchain contract orchestration/integrations.json	The doctor capability declaration replaces one toolchain digest.
ast-grep probing and validation crates/code-intel-cli/src/doctor_bootstrap/mod.rs, crates/code-intel-cli/tests/doctor_bootstrap_cli.rs	Bootstrap observations include optional ast-grep probing. Contract and CLI tests verify the tool name and boolean availability status.

Estimated code review effort: 2 (Simple) | ~10 minutes

Possibly related PRs

• 2233admin/code-intel-pipeline#13: Extends the doctor integration and updates its toolchain digest.
• 2233admin/code-intel-pipeline#15: Modifies doctor_bootstrap tool observation and integration evidence.
• 2233admin/code-intel-pipeline#70: Introduces the Rust doctor_bootstrap probe extended here for ast-grep.

Poem

I hop through the doctor’s report,
ast-grep joins the tool support.
A boolean tells if it was found,
Tests keep the contract sound.
The rabbit stamps the digest bright. 🐇

🚥 Pre-merge checks | ✅ 5

✅ Passed checks (5 passed)

Check name	Status	Explanation
Title check	✅ Passed	The title clearly identifies the main change: adding an optional ast-grep probe to doctor bootstrap.
Description check	✅ Passed	The description directly explains the ast-grep probe, its optional status, tests, digest update, and verification results.
Docstring Coverage	✅ Passed	No functions found in the changed files to evaluate docstring coverage. Skipping docstring coverage check.
Linked Issues check	✅ Passed	Check skipped because no linked issues were found for this pull request.
Out of Scope Changes check	✅ Passed	Check skipped because no linked issues were found for this pull request.

✨ Finishing Touches

📝 Generate docstrings

• Create stacked PR
• Commit on current branch

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[github-actions]

Code Intel change risk

Score	Percentile	Level
56/100	35th (vs last 49 commits)	🟢 low

Top signals

• Diff shape: 3 file(s), +64/-2 (max file share 0.82)
• Test asymmetry: source changed, tests touched
• Bug-magnet: 19 fix commit(s) in touched files (180d)
• Churn: 42 commit(s) touching these files (90d)

_{revspec: origin/main..HEAD · threshold: percentile >= 90 blocks unless labeled risk-accepted · code-intel change risk}

[coderabbitai]

🧹 Nitpick comments (1)

crates/code-intel-cli/tests/doctor_bootstrap_cli.rs (1)

251-304: 🗄️ Data Integrity & Integration | 🔵 Trivial | ⚡ Quick win

Cover the complete manifest-to-observation contract.

The test only checks that ast-grep exists, is optional in the output, and has a boolean found value. It does not compare against the capability's required field in orchestration/integrations.json, verify the emitted source, or exercise a controlled missing-tool case. A regression that drops source or always reports found: false can pass.

Capture the manifest entry, assert its required value, compare it with probed["required"], and assert that source matches found. Also assert that an absent optional tool is not added to missing.

Suggested assertions

-    let ships_ast_grep_plan = manifest["integrations"]
+    let capability = manifest["integrations"]
         .as_array()
         .expect("integrations array")
         .iter()
-        .any(|entry| entry["id"] == "edit.ast-grep-plan" && entry["runtimeAdapter"].is_string());
-    assert!(
-        ships_ast_grep_plan,
-        "edit.ast-grep-plan is no longer a shipped runtime capability; drop this test rather than weakening it"
-    );
+        .find(|entry| entry["id"] == "edit.ast-grep-plan")
+        .expect("edit.ast-grep-plan capability");
+    assert!(capability["runtimeAdapter"].is_string());
+    assert_eq!(capability["required"], json!(false));

-    assert_eq!(probed["required"], json!(false));
-    assert!(probed["found"].is_boolean());
+    assert_eq!(probed["required"], capability["required"]);
+    let found = probed["found"].as_bool().expect("found boolean");
+    let source = probed["source"].as_str().expect("source string");
+    assert_eq!(found, !source.is_empty());
+    assert!(!observation["missing"]
+        .as_array()
+        .expect("missing array")
+        .iter()
+        .any(|value| value == "ast-grep"));

🤖 Prompt for AI Agents

Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.

In `@crates/code-intel-cli/tests/doctor_bootstrap_cli.rs` around lines 251 - 304,
Strengthen the test
the_probe_list_covers_the_external_tool_a_shipped_capability_shells_out_to by
retaining the matching edit.ast-grep-plan manifest entry, reading its required
value, and asserting it matches probed["required"]. Verify the probe emits a
source consistent with probed["found"], and in the controlled missing-tool
scenario assert that ast-grep is not included in the observation's missing list
because it is optional.

🤖 Prompt for all review comments with AI agents

Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.

Nitpick comments:
In `@crates/code-intel-cli/tests/doctor_bootstrap_cli.rs`:
- Around line 251-304: Strengthen the test
the_probe_list_covers_the_external_tool_a_shipped_capability_shells_out_to by
retaining the matching edit.ast-grep-plan manifest entry, reading its required
value, and asserting it matches probed["required"]. Verify the probe emits a
source consistent with probed["found"], and in the controlled missing-tool
scenario assert that ast-grep is not included in the observation's missing list
because it is optional.

---

ℹ️ Review info

⚙️ Run configuration

Configuration used: Organization UI

Review profile: CHILL

Plan: Pro Plus

Run ID: 33cc104c-e15c-4165-809c-1fe24bd83ffb

📥 Commits

Reviewing files that changed from the base of the PR and between ade9e45 and e80d3a1.

📒 Files selected for processing (3)

• crates/code-intel-cli/src/doctor_bootstrap/mod.rs
• crates/code-intel-cli/tests/doctor_bootstrap_cli.rs
• orchestration/integrations.json