strikethroo 4.1.0 → 4.1.1

package/README.md

@@ -177,7 +177,7 @@ Then browse to the VM's IP address, for example `http://192.168.122.10:4317`; `s
 npx strikethroo validate
 ```
 
-Reads your workspace and reports internal inconsistencies -- missing or malformed plan and task frontmatter, dependencies pointing at tasks that do not exist, dependency cycles, blueprint phases and task files that disagree, duplicate ids. It only reads: nothing is written or fixed for you. Every finding is an error, so the command exits non-zero as soon as it reports one, which makes it usable as a CI step. Add `--json` for a machine-readable report on stdout, or `--workspace <path>` to point it at a workspace other than the one discovered from the current directory.
+Reads your workspace and reports internal inconsistencies -- missing or malformed plan and task frontmatter, dependencies pointing at tasks that do not exist, dependency cycles, blueprint phases and task files that disagree, duplicate ids. It only reads: nothing is written or fixed for you. Every finding is an error, so the command exits non-zero as soon as it reports one, which makes it usable as a CI step. Add `--json` for a machine-readable report on stdout, or `--workspace <path>` to point it at a workspace other than the one discovered from the current directory. A workspace without `CODE_REVIEW.md`, `schemas/self-review-v2.xsd`, or `templates/UPDATE_NOTICE_TEMPLATE.md` is valid and produces no finding for them, while a missing required file is reported. `init` and `update` restore any shipped file you deleted.
 
 | Plans board                                                 | Plan detail page                                                                                                       | Archive                                                     |
 |-------------------------------------------------------------|------------------------------------------------------------------------------------------------------------------------|-------------------------------------------------------------|
@@ -187,7 +187,7 @@ Reads your workspace and reports internal inconsistencies -- missing or malforme
 
 After blueprint execution, an optional automated code review gate runs once when a second harness is discovered. The reviewer critiques the cumulative diff against the plan's requirements and emits findings validated against a schema. The gate reports; it does not decide -- there are no severity or confidence floors, and nothing is applied automatically. You read the findings and choose what to act on.
 
-**To disable:** Edit `.ai/strikethroo/config/hooks/CODE_REVIEW.md` to empty or delete it. The gate skips cleanly with a note in the execution summary.
+**To disable:** Empty `.ai/strikethroo/config/hooks/CODE_REVIEW.md`. The gate skips cleanly with a note in the execution summary. A deleted file is restored by the next `init` or `update`.
 
 **Important:** A green review gate is not a correctness guarantee. The gate reduces exposure to the same class of error a human PR approval reduces, and leaves the same class of error behind. See [Customization](https://strikethroo.canpicasoft.com/customization.html) for limitations and configuration.
 

package/dist/__tests__/fixtures/blueprint-trailing-summary.d.ts

@@ -0,0 +1,14 @@
+/**
+ * One plan body shared by the viewer, validator, and readiness-bundle suites.
+ *
+ * The blueprint carries two phases plus the template's `### Post-phase Actions`
+ * and `### Execution Summary` subsections. `TRAILING_EXECUTION_SUMMARY` is the
+ * `## Execution Summary` section `st-execute-blueprint` appends after a run;
+ * its bullets name an existing task (01) and a nonexistent one (04). Every
+ * consumer must read the same phases with or without that trailing section.
+ */
+export declare const BLUEPRINT_SECTION = "\n## Execution Blueprint\n\n**Validation Gates:**\n- Reference: `/config/hooks/POST_PHASE.md`\n\n### Phase 1: Foundations\n**Parallel Tasks:**\n- Task 01: First\n- Task 02: Second\n\n### Phase 2: Follow-through\n**Parallel Tasks:**\n- Task 03: Third (depends on: 01, 02)\n\n### Post-phase Actions\n\nRun the validation gates after each phase.\n\n### Execution Summary\n- Total Phases: 2\n- Total Tasks: 3\n";
+export declare const TRAILING_EXECUTION_SUMMARY = "\n## Execution Summary\n\n**Status**: Completed Successfully\n**Completed Date**: 2026-10-07\n\n### Results\n- Task 03: shipped the follow-through\n- Task 04: deferred to a later plan\n\n### Noteworthy Events\n- Task 01 needed a second attempt.\n\n### Necessary follow-ups\n- None.\n";
+/** Phase membership the blueprint section alone declares. */
+export declare const EXPECTED_PHASE_TASK_IDS: number[][];
+//# sourceMappingURL=blueprint-trailing-summary.d.ts.map

package/dist/__tests__/fixtures/blueprint-trailing-summary.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"blueprint-trailing-summary.d.ts","sourceRoot":"","sources":["../../../src/__tests__/fixtures/blueprint-trailing-summary.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AAEH,eAAO,MAAM,iBAAiB,2ZAsB7B,CAAC;AAEF,eAAO,MAAM,0BAA0B,gSAetC,CAAC;AAEF,6DAA6D;AAC7D,eAAO,MAAM,uBAAuB,EAAE,MAAM,EAAE,EAAkB,CAAC"}

package/dist/__tests__/fixtures/blueprint-trailing-summary.js

@@ -0,0 +1,54 @@
+"use strict";
+/**
+ * One plan body shared by the viewer, validator, and readiness-bundle suites.
+ *
+ * The blueprint carries two phases plus the template's `### Post-phase Actions`
+ * and `### Execution Summary` subsections. `TRAILING_EXECUTION_SUMMARY` is the
+ * `## Execution Summary` section `st-execute-blueprint` appends after a run;
+ * its bullets name an existing task (01) and a nonexistent one (04). Every
+ * consumer must read the same phases with or without that trailing section.
+ */
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.EXPECTED_PHASE_TASK_IDS = exports.TRAILING_EXECUTION_SUMMARY = exports.BLUEPRINT_SECTION = void 0;
+exports.BLUEPRINT_SECTION = `
+## Execution Blueprint
+
+**Validation Gates:**
+- Reference: \`/config/hooks/POST_PHASE.md\`
+
+### Phase 1: Foundations
+**Parallel Tasks:**
+- Task 01: First
+- Task 02: Second
+
+### Phase 2: Follow-through
+**Parallel Tasks:**
+- Task 03: Third (depends on: 01, 02)
+
+### Post-phase Actions
+
+Run the validation gates after each phase.
+
+### Execution Summary
+- Total Phases: 2
+- Total Tasks: 3
+`;
+exports.TRAILING_EXECUTION_SUMMARY = `
+## Execution Summary
+
+**Status**: Completed Successfully
+**Completed Date**: 2026-10-07
+
+### Results
+- Task 03: shipped the follow-through
+- Task 04: deferred to a later plan
+
+### Noteworthy Events
+- Task 01 needed a second attempt.
+
+### Necessary follow-ups
+- None.
+`;
+/** Phase membership the blueprint section alone declares. */
+exports.EXPECTED_PHASE_TASK_IDS = [[1, 2], [3]];
+//# sourceMappingURL=blueprint-trailing-summary.js.map

package/dist/__tests__/fixtures/blueprint-trailing-summary.js.map

@@ -0,0 +1 @@
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package/dist/cli.js

@@ -19,8 +19,12 @@ const server_1 = require("./serve/server");
 const export_profile_1 = require("./export-profile");
 const workspace_1 = require("./validation/workspace");
 const update_1 = require("./update");
+const metadata_1 = require("./metadata");
 const program = new commander_1.Command();
-program.name('strikethroo').version('0.1.0').description('AI-powered task management CLI tool');
+program
+    .name('strikethroo')
+    .version((0, metadata_1.getPackageVersion)())
+    .description('AI-powered task management CLI tool');
 program
     .command('init')
     .description('Initialize a new Strikethroo project')

package/dist/cli.js.map

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package/dist/conflict-detector.d.ts

@@ -4,21 +4,37 @@
  * This file handles detection of user-modified files during init command
  * by comparing current file hashes against stored baseline hashes
  */
-import { FileConflict, InitMetadata } from './types';
+import { FileConflict } from './types';
 /**
- * Detect conflicts between user's current files and incoming package files
- * @param destDir - Destination directory (.ai/strikethroo)
- * @param templateDir - Source template directory from package
- * @param metadata - Previously stored metadata with original hashes
- * @returns Array of FileConflict objects for files that have been modified
+ * List every file under `<rootDir>/config/`, relative to `rootDir`, sorted.
+ *
+ * Shared by conflict detection and the refresh pass in `src/index.ts` so both
+ * walk the same incoming paths in the same order.
+ *
+ * @param rootDir - Workspace or template root holding a `config/` tree
+ */
+export declare function getConfigFiles(rootDir: string): Promise<string[]>;
+/**
+ * `FileConflict.originalHash` for a destination with no recorded baseline.
+ *
+ * The prompt keys its wording on it: such a file is reported as untracked,
+ * never as modified since a baseline Strikethroo does not have.
  */
-export declare function detectConflicts(destDir: string, templateDir: string, metadata: InitMetadata): Promise<FileConflict[]>;
+export declare const NO_RECORDED_BASELINE = "";
 /**
- * Check if a file has been deleted by the user
+ * Detect the incoming paths that need a decision before they are written.
+ *
+ * A destination is compared against its recorded baseline, not against the
+ * incoming file: the question is whether the user changed it. A destination
+ * with no recorded hash has nothing to compare against, so it conflicts
+ * whenever it differs from the incoming file and carries
+ * `NO_RECORDED_BASELINE`. A destination byte-identical to the incoming file is
+ * never a conflict, tracked or not; writing it would change nothing.
+ *
  * @param destDir - Destination directory (.ai/strikethroo)
- * @param relativePath - Relative path from destDir
- * @param metadata - Previously stored metadata
- * @returns true if file existed in metadata but is now deleted
+ * @param templateDir - Source template directory from package
+ * @param baseline - Recorded hashes by relative path; `{}` when no metadata
+ *   can be trusted, which makes every existing destination untracked
  */
-export declare function isFileDeleted(destDir: string, relativePath: string, metadata: InitMetadata): boolean;
+export declare function detectConflicts(destDir: string, templateDir: string, baseline: Record<string, string>): Promise<FileConflict[]>;
 //# sourceMappingURL=conflict-detector.d.ts.map

package/dist/conflict-detector.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"conflict-detector.d.ts","sourceRoot":"","sources":["../src/conflict-detector.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAIH,OAAO,EAAE,YAAY,EAAE,YAAY,EAAE,MAAM,SAAS,CAAC;AAkCrD;;;;;;GAMG;AACH,wBAAsB,eAAe,CACnC,OAAO,EAAE,MAAM,EACf,WAAW,EAAE,MAAM,EACnB,QAAQ,EAAE,YAAY,GACrB,OAAO,CAAC,YAAY,EAAE,CAAC,CA2CzB;AAED;;;;;;GAMG;AACH,wBAAgB,aAAa,CAC3B,OAAO,EAAE,MAAM,EACf,YAAY,EAAE,MAAM,EACpB,QAAQ,EAAE,YAAY,GACrB,OAAO,CAMT"}
+{"version":3,"file":"conflict-detector.d.ts","sourceRoot":"","sources":["../src/conflict-detector.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAIH,OAAO,EAAE,YAAY,EAAE,MAAM,SAAS,CAAC;AAGvC;;;;;;;GAOG;AACH,wBAAsB,cAAc,CAAC,OAAO,EAAE,MAAM,GAAG,OAAO,CAAC,MAAM,EAAE,CAAC,CAwBvE;AAED;;;;;GAKG;AACH,eAAO,MAAM,oBAAoB,KAAK,CAAC;AAEvC;;;;;;;;;;;;;;GAcG;AACH,wBAAsB,eAAe,CACnC,OAAO,EAAE,MAAM,EACf,WAAW,EAAE,MAAM,EACnB,QAAQ,EAAE,MAAM,CAAC,MAAM,EAAE,MAAM,CAAC,GAC/B,OAAO,CAAC,YAAY,EAAE,CAAC,CAyBzB"}

package/dist/conflict-detector.js

@@ -39,18 +39,22 @@ var __importStar = (this && this.__importStar) || (function () {
     };
 })();
 Object.defineProperty(exports, "__esModule", { value: true });
+exports.NO_RECORDED_BASELINE = void 0;
+exports.getConfigFiles = getConfigFiles;
 exports.detectConflicts = detectConflicts;
-exports.isFileDeleted = isFileDeleted;
 const fs = __importStar(require("fs-extra"));
 const path = __importStar(require("path"));
 const metadata_1 = require("./metadata");
 /**
- * Get all config files that should be checked for conflicts
- * @param destDir - Destination directory (.ai/strikethroo)
- * @returns Array of relative paths from destDir
+ * List every file under `<rootDir>/config/`, relative to `rootDir`, sorted.
+ *
+ * Shared by conflict detection and the refresh pass in `src/index.ts` so both
+ * walk the same incoming paths in the same order.
+ *
+ * @param rootDir - Workspace or template root holding a `config/` tree
  */
-async function getConfigFiles(destDir) {
-    const configDir = path.join(destDir, 'config');
+async function getConfigFiles(rootDir) {
+    const configDir = path.join(rootDir, 'config');
     const files = [];
     async function walkDir(dir, relativeTo) {
         const entries = await fs.readdir(dir, { withFileTypes: true });
@@ -66,65 +70,53 @@ async function getConfigFiles(destDir) {
         }
     }
     if (await fs.pathExists(configDir)) {
-        await walkDir(configDir, destDir);
+        await walkDir(configDir, rootDir);
     }
-    return files;
+    return files.sort();
 }
 /**
- * Detect conflicts between user's current files and incoming package files
+ * `FileConflict.originalHash` for a destination with no recorded baseline.
+ *
+ * The prompt keys its wording on it: such a file is reported as untracked,
+ * never as modified since a baseline Strikethroo does not have.
+ */
+exports.NO_RECORDED_BASELINE = '';
+/**
+ * Detect the incoming paths that need a decision before they are written.
+ *
+ * A destination is compared against its recorded baseline, not against the
+ * incoming file: the question is whether the user changed it. A destination
+ * with no recorded hash has nothing to compare against, so it conflicts
+ * whenever it differs from the incoming file and carries
+ * `NO_RECORDED_BASELINE`. A destination byte-identical to the incoming file is
+ * never a conflict, tracked or not; writing it would change nothing.
+ *
  * @param destDir - Destination directory (.ai/strikethroo)
  * @param templateDir - Source template directory from package
- * @param metadata - Previously stored metadata with original hashes
- * @returns Array of FileConflict objects for files that have been modified
+ * @param baseline - Recorded hashes by relative path; `{}` when no metadata
+ *   can be trusted, which makes every existing destination untracked
  */
-async function detectConflicts(destDir, templateDir, metadata) {
+async function detectConflicts(destDir, templateDir, baseline) {
     const conflicts = [];
-    const configFiles = await getConfigFiles(templateDir);
-    for (const relativePath of configFiles) {
+    for (const relativePath of await getConfigFiles(templateDir)) {
         const userFilePath = path.join(destDir, relativePath);
         const newFilePath = path.join(templateDir, relativePath);
-        // Check if file exists in user's directory
-        const userFileExists = await fs.pathExists(userFilePath);
-        if (!userFileExists) {
-            // File doesn't exist in user's directory, no conflict (new file)
-            continue;
-        }
-        // Get original hash from metadata
-        const originalHash = metadata.files[relativePath];
-        if (!originalHash) {
-            // File wasn't tracked in metadata (new file in this version), no conflict
+        if (!(await fs.pathExists(userFilePath)))
             continue;
-        }
-        // Calculate current hash of user's file
         const currentHash = await (0, metadata_1.calculateFileHash)(userFilePath);
-        // Compare current hash with original hash (NOT with new file hash)
-        // This is the CRITICAL distinction: we detect if USER has modified the file
-        if (currentHash !== originalHash) {
-            // User has modified the file since last init
-            const userFileContent = await fs.readFile(userFilePath, 'utf-8');
-            const newFileContent = await fs.readFile(newFilePath, 'utf-8');
-            conflicts.push({
-                relativePath,
-                userFileContent,
-                newFileContent,
-                originalHash,
-                currentHash,
-            });
-        }
+        if (currentHash === (await (0, metadata_1.calculateFileHash)(newFilePath)))
+            continue;
+        const originalHash = baseline[relativePath];
+        if (originalHash !== undefined && currentHash === originalHash)
+            continue;
+        conflicts.push({
+            relativePath,
+            userFileContent: await fs.readFile(userFilePath, 'utf-8'),
+            newFileContent: await fs.readFile(newFilePath, 'utf-8'),
+            originalHash: originalHash ?? exports.NO_RECORDED_BASELINE,
+            currentHash,
+        });
     }
     return conflicts;
 }
-/**
- * Check if a file has been deleted by the user
- * @param destDir - Destination directory (.ai/strikethroo)
- * @param relativePath - Relative path from destDir
- * @param metadata - Previously stored metadata
- * @returns true if file existed in metadata but is now deleted
- */
-function isFileDeleted(destDir, relativePath, metadata) {
-    const filePath = path.join(destDir, relativePath);
-    const existsInMetadata = relativePath in metadata.files;
-    const existsOnDisk = fs.pathExistsSync(filePath);
-    return existsInMetadata && !existsOnDisk;
-}
 //# sourceMappingURL=conflict-detector.js.map

package/dist/conflict-detector.js.map

@@ -1 +1 @@
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package/dist/index.d.ts.map

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package/dist/index.js

@@ -299,56 +299,113 @@ async function recordHarnessSelection(metadataPath, harnesses) {
 /**
  * Copy common template files to .ai/strikethroo directory with conflict detection
  *
+ * Each incoming `config/` path gets its own outcome, so one conflict never stops
+ * another path from being installed, refreshed, or restored. Missing or
+ * unusable metadata is not a first install: every existing destination is then
+ * untracked, and each one that differs from its incoming file needs a decision
+ * before anything is written. An empty or byte-identical tree needs none, and
+ * `force` is the only route that skips the question. The tracked tree is
+ * written first and the metadata last; a failed copy throws before
+ * `saveMetadata` runs, leaving the previous metadata in place.
+ *
  * @param sourceDir - Source template tree; defaults to the shipped
  *   `templates/strikethroo/` path, overridden by a profile staging tree
  */
 async function copyCommonTemplates(baseDir, force, sourceDir = getTemplatePath('strikethroo')) {
     const destDir = resolvePath(baseDir, '.ai/strikethroo');
     const metadataPath = resolvePath(destDir, '.init-metadata.json');
-    // Check if source template directory exists
     if (!(await exists(sourceDir))) {
         throw new Error(`Template directory not found: ${sourceDir}`);
     }
-    // Load existing metadata if present
     const existingMetadata = await (0, metadata_1.loadMetadata)(metadataPath);
-    // The ignore file is copied separately, under its final name
-    const copyOptions = {
-        overwrite: true,
-        filter: (src) => path.relative(sourceDir, src) !== WORKSPACE_IGNORE_TEMPLATE,
-    };
-    // Scenario 1: First-time init (no metadata) - copy all files
-    if (!existingMetadata) {
-        await fs.copy(sourceDir, destDir, copyOptions);
-        await copyWorkspaceIgnoreFile(sourceDir, destDir);
-        // Create initial metadata
-        await createMetadata(sourceDir, destDir, metadataPath);
-        return;
+    const baseline = existingMetadata?.files ?? {};
+    let resolutions = new Map();
+    if (!force) {
+        const conflicts = await (0, conflict_detector_1.detectConflicts)(destDir, sourceDir, baseline);
+        if (conflicts.length > 0) {
+            if (!existingMetadata) {
+                console.log(chalk_1.default.yellow('\n⚠  .init-metadata.json is missing or unusable, so nothing under config/ has a trusted baseline.'));
+            }
+            console.log(chalk_1.default.yellow(`\n⚠  ${conflicts.length} file(s) differ from the incoming version and need a decision.\n`));
+            resolutions = await (0, prompts_1.promptForConflicts)(conflicts);
+        }
     }
-    // Scenario 2: Force flag - overwrite all files
-    if (force) {
-        await fs.copy(sourceDir, destDir, copyOptions);
-        await copyWorkspaceIgnoreFile(sourceDir, destDir);
-        // Update metadata
-        await createMetadata(sourceDir, destDir, metadataPath);
-        return;
+    const outcomes = await refreshConfigTree(sourceDir, destDir, baseline, resolutions, force);
+    await copyUntrackedTemplateFiles(sourceDir, destDir);
+    await copyWorkspaceIgnoreFile(sourceDir, destDir);
+    await createMetadata(metadataPath, existingMetadata, recordBaselines(baseline, outcomes));
+}
+/**
+ * Decide and apply one outcome per incoming `config/` path.
+ */
+async function refreshConfigTree(sourceDir, destDir, baseline, resolutions, force) {
+    const outcomes = [];
+    for (const relativePath of await (0, conflict_detector_1.getConfigFiles)(sourceDir)) {
+        const sourcePath = path.join(sourceDir, relativePath);
+        const destPath = path.join(destDir, relativePath);
+        const outcome = await decideRefreshOutcome(destPath, await (0, metadata_1.calculateFileHash)(sourcePath), baseline[relativePath], resolutions.get(relativePath), force);
+        if (outcome.kind !== 'kept' && outcome.kind !== 'unchanged') {
+            await fs.copy(sourcePath, destPath, { overwrite: true });
+        }
+        outcomes.push({ relativePath, ...outcome });
     }
-    // Scenario 3: Conflict detection - check for user modifications
-    const conflicts = await (0, conflict_detector_1.detectConflicts)(destDir, sourceDir, existingMetadata);
-    if (conflicts.length === 0) {
-        await fs.copy(sourceDir, destDir, copyOptions);
-        await copyWorkspaceIgnoreFile(sourceDir, destDir);
-        // Update metadata
-        await createMetadata(sourceDir, destDir, metadataPath);
-        return;
+    return outcomes;
+}
+/**
+ * Classify one destination against its incoming file and recorded baseline.
+ *
+ * A destination that diverged from its baseline, or that has no baseline, is
+ * replaced only by `force` or an explicit `overwrite` answer; with no answer it
+ * is kept, because only the prompt may authorize destroying a file this refresh
+ * did not write. A kept destination with no baseline records none.
+ */
+async function decideRefreshOutcome(destPath, incomingHash, recordedHash, resolution, force) {
+    if (!(await exists(destPath))) {
+        return { kind: 'installed', hash: incomingHash };
     }
-    // Conflicts detected - prompt user for resolution
-    console.log(chalk_1.default.yellow(`\n⚠  Detected ${conflicts.length} modified file(s). Prompting for resolution...\n`));
-    const resolutions = await (0, prompts_1.promptForConflicts)(conflicts);
-    // Apply resolutions
-    await applyResolutions(sourceDir, destDir, resolutions);
-    await copyWorkspaceIgnoreFile(sourceDir, destDir);
-    // Update metadata for all files (including resolved conflicts)
-    await createMetadata(sourceDir, destDir, metadataPath);
+    const currentHash = await (0, metadata_1.calculateFileHash)(destPath);
+    if (currentHash === incomingHash) {
+        return { kind: 'unchanged', hash: incomingHash };
+    }
+    if (recordedHash !== undefined && currentHash === recordedHash) {
+        return { kind: 'refreshed', hash: incomingHash };
+    }
+    if (force || resolution === 'overwrite' || resolution === 'overwrite-all') {
+        return { kind: 'overwritten', hash: incomingHash };
+    }
+    return { kind: 'kept', hash: recordedHash };
+}
+/**
+ * Build the `files` map from the refresh outcomes.
+ *
+ * A recorded path the incoming tree no longer ships keeps its recorded hash:
+ * the refresh learned nothing new about it, and dropping one that is also gone
+ * from disk would erase the deletion `validate` reports. An outcome with no
+ * hash records nothing.
+ */
+function recordBaselines(baseline, outcomes) {
+    const files = { ...baseline };
+    for (const { relativePath, hash } of outcomes) {
+        if (hash !== undefined) {
+            files[relativePath] = hash;
+        }
+    }
+    return files;
+}
+/**
+ * Copy the template entries outside `config/`, such as `README.md`, verbatim.
+ *
+ * Only `config/` is hash-tracked, so these refresh on every run. The ignore
+ * template is excluded here because it lands under a different name.
+ */
+async function copyUntrackedTemplateFiles(sourceDir, destDir) {
+    await fs.copy(sourceDir, destDir, {
+        overwrite: true,
+        filter: src => {
+            const [first] = path.relative(sourceDir, src).split(path.sep);
+            return first !== 'config' && first !== WORKSPACE_IGNORE_TEMPLATE;
+        },
+    });
 }
 /**
  * Copy the workspace ignore template to its final `.gitignore` name.
@@ -368,42 +425,10 @@ async function copyWorkspaceIgnoreFile(sourceDir, destDir) {
     await fs.copy(source, path.join(destDir, WORKSPACE_IGNORE_FILE), { overwrite: true });
 }
 /**
- * Create or update metadata file with current file hashes
+ * Write the metadata for a completed refresh, carrying provenance and the
+ * harness selection forward from the previous metadata.
  */
-async function createMetadata(sourceDir, destDir, metadataPath) {
-    const existingMetadata = await (0, metadata_1.loadMetadata)(metadataPath);
-    const files = {};
-    async function walkDir(dir, relativeTo) {
-        const entries = await fs.readdir(dir, { withFileTypes: true });
-        for (const entry of entries) {
-            const fullPath = path.join(dir, entry.name);
-            const relativePath = path.relative(relativeTo, fullPath);
-            // Skip README.md (always overwrite on init/re-init)
-            if (relativePath === 'README.md') {
-                continue;
-            }
-            // Skip metadata file itself
-            if (relativePath === '.init-metadata.json') {
-                continue;
-            }
-            if (entry.isDirectory()) {
-                await walkDir(fullPath, relativeTo);
-            }
-            else if (entry.isFile()) {
-                // Calculate hash of the destination file (what we just copied)
-                const destFilePath = path.join(destDir, relativePath);
-                if (await exists(destFilePath)) {
-                    const hash = await (0, metadata_1.calculateFileHash)(destFilePath);
-                    files[relativePath] = hash;
-                }
-            }
-        }
-    }
-    const configDir = path.join(destDir, 'config');
-    if (await exists(configDir)) {
-        await walkDir(configDir, destDir);
-    }
-    // Create metadata object
+async function createMetadata(metadataPath, existingMetadata, files) {
     const metadata = {
         version: (0, metadata_1.getPackageVersion)(),
         workspaceSchemaVersion: metadata_1.CURRENT_WORKSPACE_SCHEMA_VERSION,
@@ -416,22 +441,8 @@ async function createMetadata(sourceDir, destDir, metadataPath) {
     if (existingMetadata?.harnesses) {
         metadata.harnesses = existingMetadata.harnesses;
     }
-    // Save metadata
     await (0, metadata_1.saveMetadata)(metadataPath, metadata);
 }
-/**
- * Apply user resolutions to file conflicts
- */
-async function applyResolutions(sourceDir, destDir, resolutions) {
-    for (const [relativePath, resolution] of resolutions) {
-        const sourcePath = path.join(sourceDir, relativePath);
-        const destPath = path.join(destDir, relativePath);
-        if (resolution === 'overwrite') {
-            await fs.copy(sourcePath, destPath, { overwrite: true });
-        }
-        // If 'keep', do nothing - keep user's file
-    }
-}
 /**
  * Check if a directory already has Strikethroo initialized
  */