@turri-dev/cli 0.1.3-next.f74e98a → 0.1.4-next.073df25

package/dist/regenerate/notes.js

@@ -1,5 +1,5 @@
 import { existsSync, readFileSync, rmSync, writeFileSync } from "node:fs";
-import { basename, dirname, join } from "node:path";
+import { basename, dirname, join, resolve } from "node:path";
 import { defineTool } from "@earendil-works/pi-coding-agent";
 import { Type } from "typebox";
 import { reportActivity } from "./activity.js";
@@ -40,7 +40,6 @@ export const SECTIONS = {
     where: "Where things are",
     run: "How to build, run and test",
     assumptions: "Assumptions",
-    gaps: "Spec gaps",
     pitfalls: "Pitfalls",
     pulses: "Pulses",
 };
@@ -53,8 +52,13 @@ export function notesPath(buildDir) {
     return join(buildDir, NOTES_FILE);
 }
 function empty() {
-    return { where: [], run: [], assumptions: [], gaps: [], pitfalls: [], pulses: [] };
+    return { where: [], run: [], assumptions: [], pitfalls: [], pulses: [] };
 }
+/**
+ * Sections the notes no longer have, their lines dropped as they are read: the spec gaps are the person's, reported
+ * with report_spec_gap - the choice made meanwhile is an assumption, which stays.
+ */
+const DROPPED = new Set(["spec gaps"]);
 /** The notes, as lines per section. Lines under no known heading go to pitfalls, not lost. */
 export function parseNotes(text) {
     const notes = empty();
@@ -63,11 +67,12 @@ export function parseNotes(text) {
         const line = raw.trim();
         const heading = /^##\s+(.+)$/.exec(line);
         if (heading) {
-            section = ORDER.find((key) => SECTIONS[key].toLowerCase() === heading[1].trim().toLowerCase()) ?? section;
+            const named = heading[1].trim().toLowerCase();
+            section = DROPPED.has(named) ? undefined : (ORDER.find((key) => SECTIONS[key].toLowerCase() === named) ?? section ?? "pitfalls");
             continue;
         }
         const item = /^[-*]\s+(.+)$/.exec(line);
-        if (item)
+        if (item && section !== undefined)
             notes[section].push(item[1].trim());
     }
     return notes;
@@ -93,14 +98,14 @@ const GUIDANCE = [
     `- ${SECTIONS.where}: entry points, layout, where each functionality and its tests live.`,
     `- ${SECTIONS.run}: the commands that build, run and test it, and what had to be installed for them.`,
     `- ${SECTIONS.assumptions}: what you assumed where the specification is silent - a format, a default, a`,
-    "  choice it leaves open. Build on the assumptions already there; change or remove one the moment the code",
-    "  or the specification shows it wrong.",
-    `- ${SECTIONS.gaps}: what the specification should say and does not - a behaviour you had to decide that the`,
-    "  person would want to decide, not a detail of how. Each is put to the person, to be written into the",
-    "  specification. One a line, as the question it leaves: \"What happens to a contact archived in HubSpot after it",
-    "  was synced?\"",
+    "  choice it leaves open - and the tests that assert it, when any do: \"A Dash drains Pulses at 1/s - asserted in",
+    "  predators.test.ts, The Dash\". One no test asserts is written down all the same. Build on the assumptions",
+    "  already there; change or remove one the moment the code or the specification shows it wrong - and the tests",
+    "  it names with it.",
     `- ${SECTIONS.pitfalls}: what went wrong and what fixed it, approaches that did not work.`,
     `- ${SECTIONS.pulses}: written by turri as each pulse ends - read them, never write them.`,
+    "A behaviour you had to decide that the person would want to decide - not a detail of how - is not a note: report",
+    "it with report_spec_gap, with the assumption you made meanwhile.",
     "Each line stands on its own, for someone who never saw your work. When and where it came from is added",
     "to it for you - do not write it. Where two lines disagree, the later one is right: change the older one",
     'rather than add a contradicting line. Leave a section with nothing new alone: "none" is not a note.',
@@ -232,7 +237,7 @@ export function createNotesTool(buildDir, onWrite, before = () => { }, source) {
         label: "Update notes",
         description: "Update the working notes on this codebase for the next agent - add a line, change one that is no longer " +
             "true, remove one that is wrong - in its sections: where things are, how to build, run and test, " +
-            "assumptions made where the specification is silent, spec gaps the person should decide, and pitfalls. Never " +
+            "assumptions made where the specification is silent, and pitfalls. Never " +
             "requirements: the specification is never an assumption.",
         promptSnippet: "leave the next agent what you learned and assumed about this codebase",
         parameters: Type.Object({
@@ -283,7 +288,7 @@ export function sectionNamed(name) {
 /** How many times an agent that finishes without update_notes is asked to call it. */
 export const NOTES_ASKS = 3;
 /** The turn that asks for the notes: update_notes is the only tool it may use - the work it follows is done. */
-export const NOTES_TURN = { onlyTools: ["update_notes"] };
+export const NOTES_TURN = { onlyTools: ["update_notes", "report_spec_gap"] };
 /** What the notes turn says first, once the harness's own run of `script` has passed on the work. */
 export function passedOutcome(script) {
     return (`The harness ran the project's ${script} on your work itself, and it passed: your work is done and accepted. ` +
@@ -327,10 +332,53 @@ export function recordPulse(buildDir, text, source) {
         // The notes are a help, not the work.
     }
 }
-/** The lines of a section added since `before` - a pulse's new spec gaps, say - without when and where they came from. */
-export function linesAddedSince(before, buildDir, section) {
-    const known = new Set(before[section]);
-    return readNotes(buildDir)[section].filter((line) => !known.has(line)).map((line) => line.replace(/^\[[^\]]*\]\s*/, ""));
+/** Every spec gap reported in this process, with the codebase it was met in: a pulse reads those since it started. */
+const reportedGaps = [];
+/** Where the spec gaps stand now: what `gapsSince` reads from. */
+export function gapMark() {
+    return reportedGaps.length;
+}
+/** The spec gaps reported in these codebases since `mark`. */
+export function gapsSince(mark, dirs) {
+    const wanted = new Set(dirs.map((dir) => resolve(dir)));
+    return reportedGaps.slice(mark).filter((entry) => wanted.has(entry.dir)).map((entry) => entry.gap);
+}
+/**
+ * `report_spec_gap`: a behaviour the specification leaves open that the person would want to decide, put to them as
+ * the pulse ends - never into the notes, which are the next agent's. What the agent decided meanwhile goes into the
+ * notes' assumptions, so the code built on it is known for what it is until the specification settles it.
+ */
+export function createSpecGapTool(buildDir, source) {
+    return defineTool({
+        name: "report_spec_gap",
+        label: "Report a spec gap",
+        description: "Report a spec gap: a behaviour the specification leaves open that the person would want to decide - not a detail " +
+            "of how. Decide it meanwhile and carry on: the person is asked once the work ends, and what they decide is " +
+            "written into the specification. The assumption you made is added to the notes' assumptions for you.",
+        promptSnippet: "tell the person about a behaviour the specification leaves open, and what you decided meanwhile",
+        parameters: Type.Object({
+            question: Type.String({ description: 'The question it leaves the person, one line: "What happens to a contact archived in HubSpot after it was synced?"' }),
+            assumption: Type.String({
+                description: "What you decided meanwhile, as its line in the notes' assumptions - with the tests that assert it, when any do: " +
+                    '"An archived contact is left as synced - asserted in sync.test.ts, archived contacts".',
+            }),
+        }),
+        async execute(_id, params) {
+            const question = params.question.replace(/\s+/g, " ").trim();
+            const assumption = params.assumption.replace(/\s+/g, " ").trim();
+            if (question === "" || assumption === "")
+                throw new Error("Nothing reported - a spec gap needs both the question it leaves and the assumption you made meanwhile.");
+            // However many there are, spec gaps are put to the person - never a reason to stop the pulse.
+            reportedGaps.push({ dir: resolve(buildDir), gap: { question, assumption } });
+            const known = readNotes(buildDir).assumptions.some((line) => body(line) === assumption);
+            if (!known)
+                recordNote(buildDir, "assumptions", assumption, source ?? "spec gap");
+            return {
+                content: [{ type: "text", text: `Reported. The assumption is in the notes' assumptions${known ? " already" : " now"} - do not add it again.` }],
+                details: { question, assumption },
+            };
+        },
+    });
 }
 /** The notes, for an agent that reads them but leaves none - a judge. Empty when there are none. */
 export function notesToRead(buildDir) {
@@ -367,6 +415,7 @@ export function notesForSession(buildDir, source) {
         return true;
     };
     return {
+        gapTool: createSpecGapTool(buildDir, source),
         tool: createNotesTool(buildDir, (text) => {
             written = true;
             knownNotes.set(file, text);

package/dist/regenerate/prompt.js

@@ -278,8 +278,10 @@ function itemText(serialized) {
         return item;
     const { markdown, [ACCEPTANCE_TESTS]: tests } = (item ?? {});
     const lines = [markdown ?? JSON.stringify(item)];
+    // Each test is an item of the tree, its text in its markdown - as spec-steps.ts `itemText` reads it.
+    const testText = (test) => (typeof test === "string" ? test : (test?.markdown ?? JSON.stringify(test)));
     if (Array.isArray(tests) && tests.length > 0)
-        lines.push("  <acceptance tests>", ...tests.map((test) => `  ${String(test)}`), "  </acceptance tests>");
+        lines.push("  <acceptance tests>", ...tests.map((test) => `  ${testText(test).replace(/\n/g, "\n  ")}`), "  </acceptance tests>");
     return lines.join("\n");
 }
 const indent = (text, by) => text.split("\n").map((line) => `${by}${line}`).join("\n");

package/dist/regenerate/regenerate.js

@@ -14,7 +14,7 @@ import { buildSpecDiffPrompt, describeSpecChange, reviewedSpec, sectionModules }
 import { abandonWork, recordHistory, startWork } from "./lineage.js";
 import { createWorkLedger, SUBMIT_WORK_NOTE } from "./submit-work.js";
 import { CODER_COMPACTION } from "./compaction.js";
-import { linesAddedSince, NOTES_TURN, notesForSession, passedOutcome, readNotes, recordNote, withNotes } from "./notes.js";
+import { gapMark, gapsSince, NOTES_TURN, notesForSession, passedOutcome, recordNote, withNotes } from "./notes.js";
 import { createLoopWatch, createScriptTool, failureSignature, findTestScripts, projectRootFor, requireTestScripts, runUnitScript, STUCK_ROUNDS, withoutConformance, withTestingScripts, } from "./test-scripts.js";
 import { createWebTools, WEB_TOOLS } from "./web.js";
 import { createCanItFailTool, createMyDiffTool, selfCheckNote } from "./self-check.js";
@@ -268,8 +268,8 @@ export async function renderSpecDiff(options) {
         ...(options.cases !== undefined ? { cases: options.cases } : {}),
     });
     const digestsBefore = digestFiles(buildDir);
-    // The notes as the agent finds them: what it adds - a spec gap above all - is told with the result.
-    const notesBefore = readNotes(buildDir);
+    // The spec gaps its agents report from here on are told with the result.
+    const gapsFrom = gapMark();
     /** What the debugger found, each time it was asked: the pulse's line in the notes says it. */
     const diagnosed = [];
     const runs = [];
@@ -281,9 +281,11 @@ export async function renderSpecDiff(options) {
     const work = createWorkLedger();
     // What it checks its own work with: the diff its reviewer is shown, and whether a test catches a bug - neither decides anything.
     const gate = createUnitGate(buildDir, scripts.unit);
+    // can_it_fail, for the coding agent and its reviewer: on unless mutation-testing says otherwise.
+    const mutationTesting = scripts.unit !== undefined && configForSpec(tip.plainFile).mutationTesting !== false;
     const selfChecks = [
         createMyDiffTool({ dir: buildDir, what: "code" }),
-        ...(scripts.runOn === "copy" ? [createCanItFailTool({ buildDir, script: scripts.unit })] : []),
+        ...(mutationTesting ? [createCanItFailTool({ buildDir, script: scripts.unit })] : []),
     ];
     // A server it built, it can start and try from outside - stopped when it is done.
     const services = createServiceTools({ dir: buildDir });
@@ -305,6 +307,7 @@ export async function renderSpecDiff(options) {
         cwd: buildDir,
         customTools: [
             notes.tool,
+            notes.gapTool,
             work.tool,
             ...createWebTools(),
             createScriptTool({ kind: "unit", script: scripts.unit, run: () => runUnitScript(buildDir, scripts.unit), runs, watch: loop }),
@@ -313,7 +316,7 @@ export async function renderSpecDiff(options) {
             ...fence.tools,
             createCopyResourceTool({ resources: linkedResources, dir: buildDir }),
         ],
-        tools: [...fence.names, "run_unit_tests", ...selfChecks.map((tool) => tool.name), ...services.names, "update_notes", "submit_work", "copy_resource", ...WEB_TOOLS],
+        tools: [...fence.names, "run_unit_tests", ...selfChecks.map((tool) => tool.name), ...services.names, "update_notes", "report_spec_gap", "submit_work", "copy_resource", ...WEB_TOOLS],
         model: options.model,
         label: `${moduleName} spec change coding agent`,
         role: "coding",
@@ -498,7 +501,8 @@ export async function renderSpecDiff(options) {
                 forChange: true,
                 ...(options.cases !== undefined ? { cases: options.cases } : {}),
                 label: `${moduleName} spec change`,
-                ...(scripts.runOn === "copy" ? { unitScript: scripts.unit } : {}),
+                ...(mutationTesting ? { unitScript: scripts.unit } : {}),
+                testingScript: { path: relative(root, scripts.unit), content: readFileSync(scripts.unit, "utf8") },
                 model: options.judgeModel ?? modelSpec(inheritModel(configForSpec(tip.plainFile).judgeModel, modelOnly(options.model))),
                 send: async (next) => {
                     response = await ask(executor, next, options.onDelta);
@@ -541,8 +545,8 @@ export async function renderSpecDiff(options) {
         testRemovals,
         files,
         ...(steering !== undefined && steering.steers > 0 ? { steered: [...steering.notes] } : {}),
-        // Read before a rollback takes the notes back: a gap the agent met is the person's to decide, whether it landed or not.
-        specGaps: linesAddedSince(notesBefore, buildDir, "gaps"),
+        // A gap the agent met is the person's to decide, whether it landed or not.
+        specGaps: gapsSince(gapsFrom, [buildDir]),
         diagnosed,
     };
     /** The change landed: what the code is built from is now the spec with the change in, committed with it. */
@@ -579,8 +583,10 @@ export function specGapsText(gaps) {
         return [];
     return [
         "",
-        "Spec gaps its agents met - the spec does not say, so they decided. Put each to the user, and write the ones they decide into the spec:",
-        ...gaps.map((gap) => `- ${gap}`),
+        "Spec gaps its agents met - the spec does not say, so they decided, each as an assumption in the codebase's notes. Put " +
+            "each to the user, and write the ones they decide into the spec - the pulse that builds it is told the assumption " +
+            "it replaces:",
+        ...gaps.map((gap) => `- ${gap.question} Meanwhile: ${gap.assumption}`),
     ];
 }
 /** What a rendered spec change did, for the agent and the person. */

package/dist/regenerate/regression.js

@@ -21,7 +21,7 @@ import { keepingTestsUnchanged, listFiles } from "./testing.js";
  * job ends on it: tests that pass on their own are not done until the whole suite passes with them.
  */
 /** On top of the file tools, which are fenced to the build directory by `confine.ts`. */
-const FIX_TOOLS = ["run_unit_tests", "run_conformance_tests", "update_notes"];
+const FIX_TOOLS = ["run_unit_tests", "run_conformance_tests", "update_notes", "report_spec_gap"];
 const DEFAULT_MAX_REGRESSION_ROUNDS = ATTEMPTS.regression;
 /** The module's conformance tests, when there are any: the chain's, copied up, and its own. */
 function conformanceDirs(conformanceRoot, moduleName) {
@@ -39,6 +39,7 @@ async function repairRegression(input) {
         cwd: input.buildDir,
         customTools: [
             notes.tool,
+            notes.gapTool,
             ...createWebTools(),
             ...fence.tools,
             createScriptTool({ kind: "unit", script: input.scripts.unit, run: () => runUnitScript(input.buildDir, input.scripts.unit), runs }),

package/dist/regenerate/requires.js

@@ -1,6 +1,6 @@
-import { copyFileSync, existsSync, mkdirSync, readdirSync, rmSync } from "node:fs";
+import { copyFileSync, existsSync, mkdirSync, readdirSync, readFileSync, rmSync } from "node:fs";
 import { basename, dirname, join, resolve } from "node:path";
-import { PLAIN_SOURCE_FILE_EXTENSION, plainFileParser, withParseCache } from "../plain/parser.js";
+import { IMPORT_DIRECTIVE, PLAIN_SOURCE_FILE_EXTENSION, plainFileParser, readPlainSourceMetadata, withParseCache } from "../plain/parser.js";
 import { getFrids, getInheritedFunctionalSpecs } from "../plain/spec.js";
 import { buildDirUnder, modulesRoot, projectDirOf } from "./paths.js";
 import { notesPath } from "./notes.js";
@@ -54,6 +54,59 @@ options = {}) {
     visit(resolve(plainFile), []);
     return chain;
 }
+/** The .plain files that import `plainFile` - read from beside it, and, kept in a `template/` folder, from the folder it is in. */
+function importersOf(plainFile) {
+    const file = resolve(plainFile);
+    const dir = dirname(file);
+    const name = basename(file, PLAIN_SOURCE_FILE_EXTENSION);
+    const dirs = [dir, ...(basename(dir) === "template" ? [dirname(dir)] : [])];
+    return dirs.flatMap((at) => {
+        let names;
+        try {
+            names = readdirSync(at).filter((entry) => entry.endsWith(PLAIN_SOURCE_FILE_EXTENSION));
+        }
+        catch {
+            return [];
+        }
+        return names
+            .map((entry) => join(at, entry))
+            .filter((path) => {
+            if (path === file || !resolveTemplateDirs(path).includes(dir))
+                return false;
+            try {
+                return (readPlainSourceMetadata(readFileSync(path, "utf8")).metadata[IMPORT_DIRECTIVE] ?? []).includes(name);
+            }
+            catch {
+                return false;
+            }
+        });
+    });
+}
+/**
+ * Whether a .plain file is an import module - one a .plain file imports, or one kept in a `template/` folder - rather than
+ * a module of its own. It is no codebase: its reqs and definitions are built in the modules that import it.
+ */
+export function isImportModule(plainFile) {
+    return basename(dirname(resolve(plainFile))) === "template" || importersOf(plainFile).length > 0;
+}
+/** The modules of their own that import an import module, through any import modules between. */
+export function importingModules(plainFile) {
+    const found = new Set();
+    const seen = new Set();
+    const walk = (file) => {
+        if (seen.has(file))
+            return;
+        seen.add(file);
+        for (const importer of importersOf(file)) {
+            if (isImportModule(importer))
+                walk(importer);
+            else
+                found.add(importer);
+        }
+    };
+    walk(resolve(plainFile));
+    return [...found];
+}
 /**
  * The codebase a change to `plainFile`'s module lands in: the furthest-built module whose
  * requires chain includes it, with that chain.

package/dist/regenerate/self-check.js

@@ -1,9 +1,9 @@
-import { readFileSync, writeFileSync } from "node:fs";
-import { join, relative, resolve, sep } from "node:path";
+import { readFileSync } from "node:fs";
+import { relative, resolve, sep } from "node:path";
 import { defineTool } from "@earendil-works/pi-coding-agent";
 import { Type } from "typebox";
 import { workDiff } from "./lineage.js";
-import { lastPassingMs, runOnCode } from "./test-scripts.js";
+import { lastPassingMs, runOnCode, scriptsRunInPlace } from "./test-scripts.js";
 /**
  * Tools an agent checks its own work with, before the harness and the reviewer do: the diff the reviewer is shown, and
  * whether a test catches a change to the code. Neither decides anything - the testing scripts, run by the harness, still do.
@@ -43,16 +43,23 @@ export function canItFailLimitMs(buildDir, script) {
  */
 export function createCanItFailTool(options) {
     let left = options.runs ?? CAN_IT_FAIL_RUNS;
+    // In place, the change is made to the code itself for the run, and undone after it: the scripts run on the code there.
+    const inPlace = scriptsRunInPlace(options.buildDir);
     return defineTool({
         name: "can_it_fail",
         label: "Can it fail",
         description: "Check that the unit tests catch a bug: give one change to the code that breaks a behaviour the specification " +
             "states - a value or a status changed, a check taken out, a condition turned round where it cannot make a loop run for " +
             "ever - and the unit testing script " +
-            "runs on a copy of the code with that change. The code itself is never touched. The tests should fail; if they all " +
+            (inPlace
+                ? "runs with that change made to the code, which is put back as it was once the run ends, whatever its result. "
+                : "runs on a copy of the code with that change. The code itself is never touched. ") +
+            "The tests should fail; if they all " +
             "pass, no test catches that bug. Make a change that still builds and runs: a failure only because it no longer " +
             `compiles or imports says nothing about the tests. ${options.runs ?? CAN_IT_FAIL_RUNS} runs at most.`,
-        promptSnippet: "can_it_fail: whether the unit tests catch a bug you put in a copy of the code",
+        promptSnippet: "can_it_fail: whether the unit tests catch a bug you put in the code for one run",
+        // Never beside another call: in place, an edit made while the bug is in would be undone with it.
+        executionMode: "sequential",
         parameters: Type.Object({
             file: Type.String({ description: "The code file to change, relative to the code folder" }),
             find: Type.String({ description: "Text that is in the file exactly once - the code to change" }),
@@ -83,7 +90,7 @@ export function createCanItFailTool(options) {
             left -= 1;
             let run;
             try {
-                run = await runOnCode(options.buildDir, options.script, "unit testing script, with the change", (copy) => writeFileSync(join(copy, relative(options.buildDir, path)), text.slice(0, at) + replace + text.slice(at + find.length)), canItFailLimitMs(options.buildDir, options.script));
+                run = await runOnCode(options.buildDir, options.script, "unit testing script, with the change", { file: relative(options.buildDir, path), text: text.slice(0, at) + replace + text.slice(at + find.length) }, canItFailLimitMs(options.buildDir, options.script));
             }
             catch (error) {
                 return say(error instanceof Error ? error.message : String(error));

package/dist/regenerate/test-scripts.js

@@ -297,6 +297,10 @@ export function setScriptTimeoutForTests(ms) {
  * own paths start - and whether they run on the code in place (the default), rather than on a fresh copy
  * (`testing-scripts-run-on: copy`).
  */
+/** Whether the testing scripts run on the code in `buildDir` itself, not on a copy of it. */
+export function scriptsRunInPlace(buildDir) {
+    return projectOfBuild(buildDir).inPlace;
+}
 function projectOfBuild(buildDir) {
     const parts = resolve(buildDir).split(sep);
     const index = parts.lastIndexOf("plain_modules");
@@ -401,30 +405,70 @@ const lastPassing = new Map();
 export function lastPassingMs(buildDir, script) {
     return lastPassing.get(`${resolve(buildDir)}\n${script}`);
 }
+/** Files changed in place for a run under way, and what each held: put back however the run ends - the process exiting too. */
+const changedInPlace = new Map();
+let restoreOnExit = false;
+function putBack(path) {
+    const original = changedInPlace.get(path);
+    if (original === undefined)
+        return;
+    writeFileSync(path, original);
+    changedInPlace.delete(path);
+}
+/**
+ * `run` with `change` made to the code itself, and undone once it ends - passed, failed, timed out, thrown, or the process
+ * exiting. Killed outright, the change is left: the next unit of work starts from the last commit (lineage.ts startWork).
+ */
+async function withChangeInPlace(buildDir, change, run) {
+    const path = resolve(buildDir, change.file);
+    if (changedInPlace.has(path))
+        throw new Error(`${change.file} is being changed for another run already.`);
+    if (!restoreOnExit) {
+        restoreOnExit = true;
+        process.once("exit", () => {
+            for (const changed of [...changedInPlace.keys()])
+                putBack(changed);
+        });
+    }
+    changedInPlace.set(path, readFileSync(path));
+    try {
+        writeFileSync(path, change.text);
+        return await run();
+    }
+    finally {
+        putBack(path);
+    }
+}
 /**
- * A script that takes the code folder - the unit testing script - run where the testing scripts
- * run. `change`: what to do to the fresh copy before it runs - only where there is a copy; never in place.
+ * A script that takes the code folder - the unit testing script - run where the testing scripts run. `change`: one file
+ * as it is for this run - made to the fresh copy, or, in place, to the code itself and undone once the run ends.
  */
 export async function runOnCode(buildDir, script, what, change, 
 /** A time limit of its own, in place of a test run's. */
 limitMs) {
     const project = projectOfBuild(buildDir);
+    const passed = (run, started) => {
+        if (change === undefined && run.exitCode === 0)
+            lastPassing.set(`${resolve(buildDir)}\n${script}`, Date.now() - started);
+        return run;
+    };
     if (project.inPlace) {
-        if (change !== undefined)
-            throw new Error("This runs only where the testing scripts run on a copy: here they run in place, on the code itself.");
-        return runScript(project.root, script, [resolve(buildDir)], buildDir);
+        const inPlace = () => runScript(project.root, script, [resolve(buildDir)], buildDir, limitMs !== undefined ? { limitMs } : {});
+        const started = Date.now();
+        if (change === undefined)
+            return passed(await inPlace(), started);
+        reportActivity(`  changing ${change.file} in place for the ${what} - put back once it has run`);
+        return withChangeInPlace(buildDir, change, inPlace);
     }
     const staging = stagingFor(buildDir);
     rmSync(staging.root, { recursive: true, force: true });
     ensureInModulesScratch(buildDir, staging.root);
     try {
         reportActivity(`  copying ${stageBuild(buildDir, staging.build)} files of the code for the ${what}`);
-        change?.(staging.build);
+        if (change !== undefined)
+            writeFileSync(join(staging.build, change.file), change.text);
         const started = Date.now();
-        const run = await runOnCopy(staging.root, script, [staging.build], buildDir, limitMs);
-        if (change === undefined && run.exitCode === 0)
-            lastPassing.set(`${resolve(buildDir)}\n${script}`, Date.now() - started);
-        return run;
+        return passed(await runOnCopy(staging.root, script, [staging.build], buildDir, limitMs), started);
     }
     finally {
         rmSync(staging.root, { recursive: true, force: true });

package/dist/regenerate/unit-review.js

@@ -63,6 +63,17 @@ export function unitReviewTask(options) {
         options.spec.trim(),
         "</specification>",
         "",
+        ...(options.testingScript !== undefined
+            ? [
+                "The harness runs the unit tests with this script, and it decides whether they pass. Read it for which tests it",
+                "runs and how: a test it never reaches - a file it does not pick up, a folder it does not look in - is not run, and",
+                "checks nothing.",
+                `<unit testing script path="${options.testingScript.path}">`,
+                options.testingScript.content.trimEnd(),
+                "</unit testing script>",
+                "",
+            ]
+            : []),
         ...(options.cases !== undefined ? [...codeReviewCasesBlock(options.cases), ""] : []),
         // A job that touches no functional spec is held only to that: the checks of behaviour are not its.
         ...(mechanical ? [] : ["Check that the code does what the specification states for this work:"]),
@@ -85,7 +96,7 @@ export function unitReviewTask(options) {
                 "  assertion so loose any answer passes, an expected value computed the way the code computes it.",
                 ...(options.canItFail === true
                     ? [
-                        "- A test you doubt can fail, check: can_it_fail puts a bug in a copy of the code - a condition turned round, a",
+                        "- A test you doubt can fail, check: can_it_fail puts a bug in the code for one run - a condition turned round, a",
                         "  value changed - and runs the unit tests on it. A test that still passes cannot fail: raise it as bad, with the",
                         `  bug it missed. ${REVIEWER_CAN_IT_FAIL_RUNS} runs a session: spend them on the tests the work rests on.`,
                     ]

package/dist/regenerate-cli.js

@@ -19,10 +19,15 @@ its conformance tests too when they are on.
   --start-over             start over, without asking, a codebase regenerated without a module it now requires -
                            with no terminal to ask and without it, the run stops there
   --from-scratch           delete the module's code and conformance tests (its lineage keeps them) and regenerate all of it
+  --from-scratch-chain     the same for every module of its requires chain, built again from the bottom - after
+                           modules were split or moved
   --harness-model <p/id>   config.turri.yaml's harness-model for this run: the planner and the conformance chooser
   --coding-model <p/id>    its coding-model, --model too: the agents that build; p/id:level for how hard a model thinks
   --judge-model <p/id>     its judge-model: the judge and the test review
   --review <true|false>    its review: whether the code and its tests are reviewed once they pass
+  --mutation-testing <true|false>
+                           its mutation-testing: whether the coding agent and the reviewer can put a bug in the code
+                           for one test run (can_it_fail), to see that a test catches it
   --conformance-tests <all|chosen|module|false>
                            its conformance-tests: which conformance tests are written and run
   --build-dir <dir>        as the run ends, however it ends, export the code there: the furthest-built codebase's
@@ -31,7 +36,7 @@ its conformance tests too when they are on.
                            as it starts, as each pulse ends and as it exits (docs/headless.md)
 
   PLAIN_TEMPLATE_DIRS      colon-separated template directories`;
-const { positional, options } = parseArgs(process.argv.slice(2), ["--dry-run", "--start-over", "--from-scratch"], USAGE, ["--build-dir", "--report", "--conformance-tests", "--harness-model", "--judge-model", "--review"]);
+const { positional, options } = parseArgs(process.argv.slice(2), ["--dry-run", "--start-over", "--from-scratch", "--from-scratch-chain"], USAGE, ["--build-dir", "--report", "--conformance-tests", "--harness-model", "--judge-model", "--review", "--mutation-testing"]);
 const { report, buildDir } = headlessOptions(options, true);
 const named = positional[0] ?? readProjectConfig(process.cwd()).module;
 // Functional specs named after the file: regenerated again though their spec did not change.
@@ -40,9 +45,10 @@ if (!named) {
     console.error(`${USAGE}\n\nNo file given, and ${CONFIG_FILE} names no module.`);
     process.exit(1);
 }
+const scratch = options["from-scratch-chain"] !== undefined ? "chain" : options["from-scratch"] !== undefined ? "module" : undefined;
 // A dry run starts nothing, and from scratch deletes before it plans: the two do not go together.
-if (options["from-scratch"] !== undefined && options["dry-run"] !== undefined) {
-    console.error("--from-scratch deletes the module's code before anything is planned: it cannot be a dry run.");
+if (scratch !== undefined && options["dry-run"] !== undefined) {
+    console.error(`--from-scratch${scratch === "chain" ? "-chain" : ""} deletes the code before anything is planned: it cannot be a dry run.`);
     process.exit(1);
 }
 runLoop({
@@ -54,8 +60,8 @@ runLoop({
     startOver: options["start-over"] !== undefined,
     ask: (loop) => again.length > 0
         ? loop.regenerateAgain(named, again)
-        : options["from-scratch"] !== undefined
-            ? loop.fromScratch(named)
+        : scratch !== undefined
+            ? loop.fromScratch(named, { chain: scratch === "chain" })
             : loop.bringUp(named),
 }).catch((error) => {
     console.error(error instanceof Error ? error.message : error);

package/dist/release-tools.js

@@ -142,7 +142,7 @@ export function createDeployTools(options) {
         },
     });
     // The one halt: with the pulses in the conversation, and without them for the release agent.
-    const stopTool = haltTool(options.jobs !== undefined ? { jobs: options.jobs } : {});
+    const stopTool = haltTool(options.jobs !== undefined ? { jobs: options.jobs, ...(options.workLoop !== undefined ? { workLoop: options.workLoop } : {}) } : {});
     return [deploy, startTool, stopTool];
 }
 export const DEPLOY_TOOLS = ["release", "activate", "halt"];

package/dist/resume-line.js

@@ -0,0 +1,4 @@
+/** pi's line on the way out that says how to resume the session, with turri in place of pi as the command to run. */
+export function resumeLine(text) {
+    return text.replace(/^((?:\x1b\[[0-9;]*m)*To resume this session:(?:\x1b\[[0-9;]*m)*\s+)pi(?= )/m, "$1turri");
+}

package/dist/review/live.js

@@ -79,7 +79,8 @@ export function createLiveReviewer(opts) {
             pending.push(finding);
             all.push(finding);
         }
-        if (violations.length === 0) {
+        // No verdict - its turn stopped before it gave one - clears nothing: the scope is looked at again next pass.
+        if (captured !== undefined && violations.length === 0) {
             cleared.push(scope);
         }
         else if (captured?.question) {