claude-setup 1.1.5 → 1.1.7

package/dist/commands/sync.js

@@ -1,12 +1,11 @@
 import { writeFileSync, mkdirSync, existsSync, readFileSync } from "fs";
 import { join } from "path";
-import { glob } from "glob";
 import { collectProjectFiles } from "../collect.js";
 import { readState } from "../state.js";
 import { readManifest, sha256, updateManifest } from "../manifest.js";
 import { buildSyncCommand } from "../builder.js";
-import { createSnapshot, collectFilesForSnapshot } from "../snapshot.js";
-import { estimateTokens, estimateCost, formatCost, formatTokenReport, buildTokenEstimate, generateHints, getTokenHookScript, formatRealCostSummary } from "../tokens.js";
+import { createSnapshot, collectFilesForSnapshot, readTimeline, readNodeData } from "../snapshot.js";
+import { estimateTokens, estimateCost, formatTokenReport, buildTokenEstimate, getTokenHookScript } from "../tokens.js";
 import { loadConfig } from "../config.js";
 import { c, section } from "../output.js";
 function ensureDir(dir) {
@@ -14,12 +13,10 @@ function ensureDir(dir) {
         mkdirSync(dir, { recursive: true });
 }
 function installTokenHook(cwd = process.cwd()) {
-    // Write the hook script
     const hooksDir = join(cwd, ".claude", "hooks");
     if (!existsSync(hooksDir))
         mkdirSync(hooksDir, { recursive: true });
     writeFileSync(join(hooksDir, "track-tokens.cjs"), getTokenHookScript(), "utf8");
-    // Merge Stop hook into settings.json
     const settingsPath = join(cwd, ".claude", "settings.json");
     let settings = {};
     if (existsSync(settingsPath)) {
@@ -31,13 +28,11 @@ function installTokenHook(cwd = process.cwd()) {
     const hookEntry = {
         hooks: [{ type: "command", command: "node \".claude/hooks/track-tokens.cjs\"" }]
     };
-    // Merge into settings.hooks.Stop
     if (!settings.hooks)
         settings.hooks = {};
     const hooks = settings.hooks;
     if (!Array.isArray(hooks.Stop))
         hooks.Stop = [];
-    // Only add if not already present
     const alreadyPresent = hooks.Stop.some(e => Array.isArray(e.hooks) && e.hooks.some((h) => typeof h.command === "string" && h.command.includes("track-tokens")));
     if (!alreadyPresent) {
         hooks.Stop.push(hookEntry);
@@ -51,7 +46,11 @@ function truncate(content, maxChars) {
         return content;
     return content.slice(0, maxChars) + "\n[... truncated for sync diff]";
 }
-function computeDiff(snapshot, collected, cwd) {
+/**
+ * Legacy diff — compares manifest hashes against collected files.
+ * Only used when no snapshot data is available (e.g., old projects).
+ */
+function computeLegacyDiff(snapshot, collected, cwd) {
     const current = {
         ...collected.configs,
         ...Object.fromEntries(collected.source.map(f => [f.path, f.content])),
@@ -60,7 +59,6 @@ function computeDiff(snapshot, collected, cwd) {
     const changed = [];
     const deleted = [];
     for (const [path, content] of Object.entries(current)) {
-        // Skip virtual keys — they're not real files
         if (path === "__digest__")
             continue;
         const hash = sha256(content);
@@ -71,57 +69,58 @@ function computeDiff(snapshot, collected, cwd) {
             changed.push({ path, current: truncate(content, 2000) });
         }
     }
-    // BUG 1 FIX: Verify file existence on disk before reporting deletions.
-    // Files may appear "deleted" because they weren't in the current collection set
-    // (different collect mode, or CLI-managed files like CLAUDE.md/settings.json).
-    // If the file still exists on disk, it was "modified outside the CLI", not deleted.
     for (const path of Object.keys(snapshot)) {
-        // Skip virtual keys
         if (path === "__digest__")
             continue;
         if (!current[path]) {
-            // Check if file actually exists on disk
             const fullPath = join(cwd, path);
             if (existsSync(fullPath)) {
-                // File exists but wasn't in our collection — it was modified outside CLI
-                // Read it and check if its hash changed
                 try {
                     const diskContent = readFileSync(fullPath, "utf8");
                     const diskHash = sha256(diskContent);
                     if (snapshot[path] !== diskHash) {
                         changed.push({ path, current: truncate(diskContent, 2000) });
                     }
-                    // If hash matches, file is unchanged — don't report anything
                 }
                 catch {
-                    // Can't read — treat as changed
                     changed.push({ path, current: "[file exists but could not be read]" });
                 }
             }
             else {
-                // File genuinely does not exist on disk — truly deleted
                 deleted.push(path);
             }
         }
     }
     return { added, changed, deleted };
 }
-async function collectClaudeInternalFiles(cwd) {
-    const files = [];
-    try {
-        const skillFiles = await glob(".claude/skills/**/*.md", { cwd, posix: true });
-        const allCmds = await glob(".claude/commands/*.md", { cwd, posix: true });
-        const commandFiles = allCmds.filter(f => !f.split("/").pop().startsWith("stack-"));
-        for (const f of [...skillFiles, ...commandFiles]) {
-            try {
-                const content = readFileSync(join(cwd, f), "utf8");
-                files.push({ path: f, content });
+/**
+ * Full-scan diff — compares every file on disk against a reference snapshot.
+ * This is the authoritative diff: catches ALL file changes, no sampling.
+ */
+function computeFullDiff(currentFiles, referenceFiles) {
+    const added = [];
+    const changed = [];
+    const deleted = [];
+    const currentPathSet = new Set();
+    for (const f of currentFiles) {
+        currentPathSet.add(f.path);
+        if (!referenceFiles[f.path]) {
+            added.push({ path: f.path, content: truncate(f.content, 2000) });
+        }
+        else {
+            const currentHash = sha256(f.content);
+            const refHash = sha256(referenceFiles[f.path]);
+            if (currentHash !== refHash) {
+                changed.push({ path: f.path, current: truncate(f.content, 2000) });
             }
-            catch { /* skip unreadable */ }
         }
     }
-    catch { /* skip */ }
-    return files;
+    for (const path of Object.keys(referenceFiles)) {
+        if (!currentPathSet.has(path)) {
+            deleted.push(path);
+        }
+    }
+    return { added, changed, deleted };
 }
 export async function runSync(opts = {}) {
     const dryRun = opts.dryRun ?? false;
@@ -133,11 +132,10 @@ export async function runSync(opts = {}) {
     const lastRun = manifest.runs.at(-1);
     const cwd = process.cwd();
     const config = loadConfig(cwd);
-    // Apply --budget override if provided
     if (opts.budget) {
         config.tokenBudget.sync = opts.budget;
     }
-    // --- Out-of-band edit detection ---
+    // --- Out-of-band edit detection (early warning) ---
     const managedFiles = [
         { label: "CLAUDE.md", path: join(cwd, "CLAUDE.md"), snapshotKey: "CLAUDE.md" },
         { label: ".mcp.json", path: join(cwd, ".mcp.json"), snapshotKey: ".mcp.json" },
@@ -161,39 +159,39 @@ export async function runSync(opts = {}) {
     }
     if (oobDetected)
         console.log("");
-    const collected = await collectProjectFiles(cwd, "normal");
-    const diff = computeDiff(lastRun.snapshot, collected, cwd);
-    // Bug 3 fix: Also detect changes inside .claude/ (skills, commands)
-    const claudeInternalFiles = await collectClaudeInternalFiles(cwd);
-    for (const f of claudeInternalFiles) {
-        const hash = sha256(f.content);
-        if (!lastRun.snapshot[f.path]) {
-            diff.added.push({ path: f.path, content: truncate(f.content, 2000) });
-        }
-        else if (lastRun.snapshot[f.path] !== hash) {
-            diff.changed.push({ path: f.path, current: truncate(f.content, 2000) });
-        }
+    // --- Full project scan (single scan, used for both diff and snapshot) ---
+    const currentFiles = collectFilesForSnapshot(cwd, []);
+    // --- Determine reference snapshot ---
+    // After restore: compare against the restored-to snapshot
+    // Normal: compare against the latest snapshot
+    const timeline = readTimeline(cwd);
+    const referenceNodeId = timeline.restoredTo ?? timeline.nodes.at(-1)?.id;
+    let referenceFiles = null;
+    if (referenceNodeId) {
+        const data = readNodeData(cwd, referenceNodeId);
+        if (data)
+            referenceFiles = data.files;
+    }
+    // --- Compute diff ---
+    let diff;
+    if (referenceFiles) {
+        // Full-scan comparison (authoritative — catches ALL changes)
+        diff = computeFullDiff(currentFiles, referenceFiles);
     }
-    // Also detect deleted .claude/ files (were in snapshot but no longer exist)
-    for (const path of Object.keys(lastRun.snapshot)) {
-        if ((path.startsWith(".claude/skills/") || (path.startsWith(".claude/commands/") && !path.split("/").pop().startsWith("stack-"))) && !path.includes("__digest__")) {
-            const alreadyInDiff = diff.added.some(f => f.path === path) ||
-                diff.changed.some(f => f.path === path) ||
-                diff.deleted.includes(path);
-            if (!alreadyInDiff && !claudeInternalFiles.some(f => f.path === path)) {
-                if (!existsSync(join(cwd, path))) {
-                    diff.deleted.push(path);
-                }
-            }
-        }
+    else {
+        // Legacy fallback — no snapshot data available
+        const collected = await collectProjectFiles(cwd, "normal");
+        diff = computeLegacyDiff(lastRun.snapshot, collected, cwd);
     }
-    if (!diff.added.length && !diff.changed.length && !diff.deleted.length && !oobDetected) {
+    const hasChanges = diff.added.length > 0 || diff.changed.length > 0 || diff.deleted.length > 0 || oobDetected;
+    if (!hasChanges) {
         console.log(`${c.green("✅")} No changes since ${c.dim(lastRun.at)}. Setup is current.`);
         return;
     }
+    // --- Build sync command (needs collected project context for template) ---
+    const collected = await collectProjectFiles(cwd, "normal");
     const state = await readState();
     const content = buildSyncCommand(diff, collected, state);
-    // Token tracking
     const tokens = estimateTokens(content);
     const cost = estimateCost(tokens);
     if (dryRun) {
@@ -214,57 +212,23 @@ export async function runSync(opts = {}) {
                 console.log(`    ${f}`);
         }
         console.log(`\n  Would write: .claude/commands/stack-sync.md (~${tokens.toLocaleString()} tokens)`);
-        // Token cost display
         section("Token cost estimate");
         const estimate = buildTokenEstimate([{ label: "sync command", content }]);
         console.log(formatTokenReport(estimate));
         return;
     }
-    // Add .claude/ internal files to snapshot
-    for (const f of claudeInternalFiles) {
-        collected.configs[f.path] = f.content;
-    }
     ensureDir(".claude/commands");
     writeFileSync(".claude/commands/stack-sync.md", content, "utf8");
     await updateManifest("sync", collected, { estimatedTokens: tokens, estimatedCost: cost });
     installTokenHook();
-    // Feature A: Create snapshot node
-    const allPaths = [
-        ...Object.keys(collected.configs),
-        ...collected.source.map(s => s.path),
-        ...claudeInternalFiles.map(f => f.path),
-    ];
-    const snapshotFiles = collectFilesForSnapshot(cwd, allPaths);
-    const changeCount = diff.added.length + diff.changed.length + diff.deleted.length;
-    createSnapshot(cwd, "sync", snapshotFiles, {
+    // Create snapshot — reuse the full scan data (no second scan needed)
+    createSnapshot(cwd, "sync", currentFiles, {
         summary: `+${diff.added.length} added, ~${diff.changed.length} modified, -${diff.deleted.length} deleted`,
     });
     console.log(`
 Changes since ${c.dim(lastRun.at)}:
   ${c.green(`+${diff.added.length}`)} added  ${c.yellow(`~${diff.changed.length}`)} modified  ${c.red(`-${diff.deleted.length}`)} deleted
 
-${c.green("✅")} Ready. Open Claude Code and run:
-   ${c.cyan("/stack-sync")}
+${c.green("✅")} Run ${c.cyan("/stack-sync")} in Claude Code to apply.
   `);
-    // Token cost display
-    section("Token cost");
-    const realSummary = formatRealCostSummary(cwd);
-    if (realSummary) {
-        console.log(realSummary);
-        console.log(`  ${c.dim(`This command estimate: ~${tokens.toLocaleString()} input tokens (${formatCost(cost)})`)}`);
-    }
-    else {
-        console.log(`  ~${tokens.toLocaleString()} input tokens (${c.dim(`${formatCost(cost)}`)})`);
-        console.log(`  ${c.dim("Estimates only — real costs tracked after first Claude Code session")}`);
-    }
-    // Optimization hints
-    const runs = manifest.runs.map(r => ({ command: r.command, estimatedTokens: r.estimatedTokens }));
-    const hints = generateHints(runs, tokens, config.tokenBudget.sync);
-    if (hints.length) {
-        section("Optimization hints");
-        for (const hint of hints) {
-            console.log(`  ${c.yellow("💡")} ${hint}`);
-        }
-    }
-    console.log("");
 }

package/dist/doctor.js

@@ -375,9 +375,14 @@ export async function runDoctor(verbose = false, fix = false, testHooks = false)
                         counts.warnings++;
                     }
                     else if (result.status === "error") {
+                        const stderr = result.stderr ?? "";
+                        const isFileMissing = stderr.includes("Cannot find module") || stderr.includes("MODULE_NOT_FOUND");
+                        const hint = isFileMissing
+                            ? `\n      Hint: hook file not found — run ${c.cyan("npx claude-setup init")} to reinstall it.`
+                            : "";
                         statusLine("⚠️ ", label, c.yellow(`FAIL (exit ${result.exitCode}, ${result.timeMs}ms)\n` +
-                            `      Command: ${hook.command.slice(0, 50)}\n` +
-                            `      ${result.stderr ? `stderr: ${result.stderr.slice(0, 100)}` : ""}`));
+                            `      Command: ${hook.command.slice(0, 60)}\n` +
+                            `      ${stderr ? `stderr: ${stderr.slice(0, 200)}` : ""}${hint}`));
                         counts.warnings++;
                     }
                     else if (result.status === "permission") {
@@ -409,13 +414,13 @@ export async function runDoctor(verbose = false, fix = false, testHooks = false)
                     counts.healthy++;
                 }
                 else if (isInTemplate) {
-                    statusLine("🔴", `\${${v}}`, c.red(`NOT SET — MCP server will fail at runtime.\n` +
+                    statusLine("🔴", `\${${v}}`, c.red(`NOT SET — MCP server will fail at runtime and won't appear in /mcp.\n` +
                         `      Documented in .env.example but not loaded into environment.\n` +
                         `      Fix: set ${v} in your shell or .env file, then restart Claude Code.`));
                     counts.critical++;
                 }
                 else {
-                    statusLine("🔴", `\${${v}}`, c.red(`NOT SET — MCP server will fail at runtime.\n` +
+                    statusLine("🔴", `\${${v}}`, c.red(`NOT SET — MCP server will fail at runtime and won't appear in /mcp.\n` +
                         `      Missing from both environment and .env.example.\n` +
                         `      Fix: add ${v} to .env.example and set its value in your shell or .env file.`));
                     counts.critical++;

package/dist/index.js

@@ -1,5 +1,6 @@
 #!/usr/bin/env node
 import { Command } from "commander";
+import { createInterface } from "readline";
 import { createRequire } from "module";
 import { runInit } from "./commands/init.js";
 import { runAdd } from "./commands/add.js";
@@ -10,6 +11,7 @@ import { runRemove } from "./commands/remove.js";
 import { runRestore } from "./commands/restore.js";
 import { runCompare } from "./commands/compare.js";
 import { runExport } from "./commands/export.js";
+import { c } from "./output.js";
 const require = createRequire(import.meta.url);
 const pkg = require("../package.json");
 const program = new Command();
@@ -24,9 +26,9 @@ program
     .option("--template <path>", "Apply a template instead of scanning (local path or URL)")
     .action((opts) => runInit({ dryRun: opts.dryRun, template: opts.template }));
 program
-    .command("add")
+    .command("add [input...]")
     .description("Add a multi-file capability")
-    .action(runAdd);
+    .action((input) => runAdd({ input: input?.length ? input.join(" ") : undefined }));
 program
     .command("sync")
     .description("Update setup after project changes")
@@ -49,23 +51,51 @@ program
     testHooks: opts.testHooks,
 }));
 program
-    .command("remove")
+    .command("remove [input...]")
     .description("Remove a capability cleanly")
-    .action(runRemove);
-// Feature A: Time-travel snapshot commands
+    .action((input) => runRemove({ input: input?.length ? input.join(" ") : undefined }));
 program
     .command("restore")
     .description("Jump to any snapshot node, restore files to that state")
-    .action(runRestore);
+    .option("--list", "Show snapshot timeline without prompting")
+    .option("--id <snapshotId>", "Restore directly to a specific snapshot ID")
+    .action((opts) => runRestore({ list: opts.list, id: opts.id }));
 program
     .command("compare")
     .description("Diff between any two snapshot nodes to see what changed")
     .action(runCompare);
-// Feature H: Config template export
 program
     .command("export")
     .description("Save current project config as a reusable template")
     .action(runExport);
-// Default action when no command given
-program.action(() => runInit({}));
+// Default action — interactive menu when no command given
+program.action(async () => {
+    const choices = [
+        { key: "1", label: "init", desc: "Full project setup", run: () => runInit({}) },
+        { key: "2", label: "add", desc: "Add a capability", run: () => runAdd({}) },
+        { key: "3", label: "sync", desc: "Update after changes", run: () => runSync({}) },
+        { key: "4", label: "status", desc: "Show current state", run: () => runStatus() },
+        { key: "5", label: "doctor", desc: "Validate environment", run: () => runDoctorCommand({}) },
+        { key: "6", label: "restore", desc: "Time-travel to snapshot", run: () => runRestore({}) },
+        { key: "7", label: "compare", desc: "Diff between snapshots", run: () => runCompare() },
+        { key: "8", label: "remove", desc: "Remove a capability", run: () => runRemove({}) },
+        { key: "9", label: "export", desc: "Save as template", run: () => runExport() },
+    ];
+    console.log(`\n${c.bold("Claude Setup")} ${c.dim(`v${pkg.version}`)}\n`);
+    for (const ch of choices) {
+        console.log(`  ${c.cyan(ch.key)}  ${ch.label.padEnd(10)} ${c.dim(ch.desc)}`);
+    }
+    console.log("");
+    const rl = createInterface({ input: process.stdin, output: process.stdout });
+    const answer = await new Promise(resolve => {
+        rl.question(`  ${c.bold("Choose (1-9):")} `, a => { rl.close(); resolve(a.trim()); });
+    });
+    const choice = choices.find(ch => ch.key === answer || ch.label === answer.toLowerCase());
+    if (!choice) {
+        console.log(`\n  Invalid choice. Run ${c.cyan("npx claude-setup <command>")} or pick 1-9.\n`);
+        return;
+    }
+    console.log("");
+    await choice.run();
+});
 program.parse();

package/dist/marketplace.js

@@ -138,11 +138,12 @@ export function buildMarketplaceInstructions(input) {
     lines.push(``);
     lines.push(`NOTE: /plugin marketplace add FAILS for this repo (one entry has broken schema).`);
     lines.push(`Use the DIRECT FETCH approach below instead — no marketplace add needed.`);
+    lines.push(`If the curl command fails or returns an error, skip to STEP 3 immediately — do NOT stop.`);
     lines.push(``);
     lines.push(`**2a. Fetch catalog and find matching plugin:**`);
     lines.push(`\`\`\`bash`);
     lines.push(`curl -s "${MARKETPLACE_CATALOG_URL}" \\`);
-    lines.push(`  | node -e "const d=JSON.parse(require('fs').readFileSync('/dev/stdin','utf8'));const q='${categoryFilter}';const r=d.plugins.filter(p=>(!q||p.category.includes(q))&&p.name&&p.source).slice(0,5).map(p=>({name:p.name,source:p.source,desc:p.description}));console.log(JSON.stringify(r,null,2));"`);
+    lines.push(`  | node -e "const d=JSON.parse(require('fs').readFileSync(0,'utf8'));const q='${categoryFilter}';const r=d.plugins.filter(p=>(q===''||p.category.includes(q))&&p.name&&p.source).slice(0,10).map(p=>({name:p.name,source:p.source,desc:p.description}));console.log(JSON.stringify(r,null,2));"`);
     lines.push(`\`\`\``);
     lines.push(``);
     lines.push(`**2b. Pick the best match — get its source path (e.g. \`./plugins/productivity/my-skill\`)**`);
@@ -152,7 +153,7 @@ export function buildMarketplaceInstructions(input) {
     lines.push(`# Replace PLUGIN_SOURCE_PATH with value from step 2b (e.g. plugins/productivity/my-skill)`);
     lines.push(`PLUGIN_SOURCE_PATH="plugins/productivity/my-skill"`);
     lines.push(`curl -s "https://api.github.com/repos/${MARKETPLACE_REPO}/contents/\${PLUGIN_SOURCE_PATH}/skills" \\`);
-    lines.push(`  | node -e "const a=JSON.parse(require('fs').readFileSync('/dev/stdin','utf8'));console.log(a.map(x=>x.name).join('\\n'));"`);
+    lines.push(`  | node -e "const a=JSON.parse(require('fs').readFileSync(0,'utf8'));console.log(a.map(x=>x.name).join('\\n'));"`);
     lines.push(`\`\`\``);
     lines.push(``);
     lines.push(`**2d. For each skill listed, download and install it:**`);

package/dist/snapshot.d.ts

@@ -19,6 +19,7 @@ export interface SnapshotNode {
     input?: string;
     changedFiles: string[];
     summary: string;
+    fullSnapshot?: boolean;
 }
 export interface SnapshotTimeline {
     nodes: SnapshotNode[];
@@ -41,9 +42,14 @@ export declare function createSnapshot(cwd: string, command: string, changedFile
     summary?: string;
 }): SnapshotNode;
 /**
- * Build the cumulative file state at a given node by accumulating
- * all files from node 0 through the target node. Later nodes override
- * earlier ones (last-write-wins), giving the full state at that point.
+ * Build the complete file state at a given node.
+ *
+ * Full snapshots (fullSnapshot: true) store the entire project state — used directly.
+ * Legacy delta snapshots accumulate from node 0 to target (last-write-wins).
+ *
+ * Why the distinction matters: with delta snapshots, if a file was deleted between A→B,
+ * it would wrongly appear in cumulative state at B (still present from A). Full snapshots
+ * avoid this because the target node's data IS the complete truth at that point.
  */
 export declare function buildCumulativeState(cwd: string, nodeId: string, timeline: SnapshotTimeline): Record<string, string> | null;
 /**
@@ -56,6 +62,7 @@ export declare function buildCumulativeState(cwd: string, nodeId: string, timeli
 export declare function restoreSnapshot(cwd: string, nodeId: string, timeline?: SnapshotTimeline): {
     restored: string[];
     failed: string[];
+    deleted: string[];
     stale: string[];
 };
 /**
@@ -76,10 +83,11 @@ export declare function compareSnapshots(cwd: string, nodeIdA: string, nodeIdB:
     identical: string[];
 };
 /**
- * Collect current file contents for snapshot.
- * Reads tracked files + CLI-managed files from disk.
+ * Collect ALL project files for snapshot — full git-like coverage.
+ * Respects .gitignore + hard exclusions (node_modules, .git, binaries, .env).
+ * The trackedPaths param is kept for API compat but ignored.
  */
-export declare function collectFilesForSnapshot(cwd: string, trackedPaths: string[]): Array<{
+export declare function collectFilesForSnapshot(cwd: string, _trackedPaths: string[]): Array<{
     path: string;
     content: string;
 }>;