@kodrunhq/claudefy 1.4.0 → 1.4.2

package/README.md

@@ -6,6 +6,10 @@
   <img src="https://img.shields.io/badge/TypeScript-strict-blue?logo=typescript&logoColor=white" alt="TypeScript" />
 </p>
 
+<p align="center">
+  <img src="assets/logo.svg" alt="claudefy logo" width="120" height="120" />
+</p>
+
 <h1 align="center">claudefy</h1>
 
 <p align="center">
@@ -15,14 +19,15 @@
 
 ---
 
-claudefy keeps your `~/.claude` directory — commands, skills, agents, hooks, rules, plans, plugins, settings, and project configs — in sync across all your machines through a private git repository. It encrypts sensitive content with AES-256-SIV, normalizes machine-specific paths, deep-merges settings, and can run fully automatically via Claude Code hooks.
+claudefy keeps your `~/.claude` directory — CLAUDE.md, MEMORY.md, commands, skills, agents, hooks, rules, plans, plugins, settings, and project configs — in sync across all your machines through a private git repository. It also selectively syncs MCP server configurations from `~/.claude.json`. It encrypts sensitive content with AES-256-SIV, normalizes machine-specific paths, deep-merges settings, and can run fully automatically via Claude Code hooks.
 
 ## Why claudefy?
 
 - **One config, every machine.** Stop manually copying files between your laptop, desktop, and servers.
 - **Safe by design.** Credentials never leave your machine. Secrets are detected and encrypted before push. Remote hooks are stripped on pull to prevent injection.
 - **Set it and forget it.** With auto-sync hooks, `pull` runs when Claude Code starts and `push` runs when it ends. No manual steps.
-- **Conflict-free.** Per-machine git branches prevent collisions. Deep merge resolves settings.json at the key level.
+- **Conflict-free.** Per-machine git branches prevent collisions. Deep merge resolves settings.json at the key level, preserving local permission rules.
+- **Preview before you sync.** `claudefy diff` shows exactly what would change. `--dry-run` on push/pull lets you verify before committing.
 
 ## Quick Start
 
@@ -56,50 +61,28 @@ That's it. With `--hooks`, sync is automatic from now on.
 claudefy push     # push local changes
 claudefy pull     # pull remote changes
 claudefy status   # see what would sync
+claudefy diff     # preview what push/pull would change
 ```
 
 ## How It Works
 
-```
-                        ┌────────────────┐
-                        │  Private Git   │
-                        │   Repository   │
-                        └──────┬─────────┘
-                               │
-              ┌────────────────┼────────────────┐
-              │                │                │
-      ┌───────▼──────┐ ┌──────▼───────┐ ┌──────▼───────┐
-      │  Machine A   │ │  Machine B   │ │  Machine C   │
-      │ branch: m/A  │ │ branch: m/B  │ │ branch: m/C  │
-      └───────┬──────┘ └──────┬───────┘ └──────┬───────┘
-              │                │                │
-         ~/.claude        ~/.claude        ~/.claude
-```
+<p align="center">
+  <img src="assets/architecture.svg" alt="claudefy architecture" width="720" />
+</p>
 
 Each machine gets its own git branch (`machines/<id>`). Push merges into `main`; pull merges `main` back into the machine branch. No conflicts, no data loss.
 
-### Push pipeline
-
-```
-~/.claude  →  SyncFilter  →  PathMapper  →  SecretScanner  →  Encryptor  →  Git push
-             (allow/deny)   (normalize)    (detect secrets)   (AES-SIV)
-```
-
-### Pull pipeline
-
-```
-Git pull  →  Decrypt  →  PathMapper  →  Merger  →  SecurityFilter  →  ~/.claude
-                         (remap)      (deep merge)  (strip hooks)
-```
-
 ## What Gets Synced
 
 | | Items | Notes |
 |---|-------|-------|
-| **Synced** | commands, agents, skills, hooks, rules, plans, plugins, agent-memory, projects, settings.json, history.jsonl, package.json | Core config that travels with you |
-| **Never synced** | cache, backups, file-history, shell-snapshots, paste-cache, session-env, tasks, .credentials.json | Machine-local or sensitive |
+| **Always synced** | CLAUDE.md, MEMORY.md, commands, agents, skills, hooks, rules, plans, plugins, agent-memory, projects, settings.json, history.jsonl, package.json | Core config that travels with you |
+| **Selectively synced** | `~/.claude.json` mcpServers (opt-in), theme, notification preferences | Requires `claudeJson.syncMcpServers: true` for MCP servers |
+| **Never synced** | cache, backups, file-history, shell-snapshots, paste-cache, session-env, tasks, .credentials.json, settings.local.json, statsig, telemetry, ide, debug, todos, stats-cache.json | Machine-local, ephemeral, or sensitive |
 | **Unknown** | Anything else | Synced to separate dir, always encrypted when encryption is enabled |
 
+> **Note:** `settings.local.json` is hardcoded as never-synced — it cannot be overridden even with a custom allowlist. This follows Claude Code's `.local.` convention for non-shared files.
+
 ## Commands
 
 ### Core
@@ -110,6 +93,7 @@ Git pull  →  Decrypt  →  PathMapper  →  Merger  →  SecurityFilter  →
 | `claudefy join --backend <url>` | Join from another machine |
 | `claudefy push` | Push local changes to remote |
 | `claudefy pull` | Pull remote changes to local |
+| `claudefy diff` | Preview what push/pull would change |
 | `claudefy override --confirm` | Wipe remote, push local as source of truth |
 | `claudefy status` | Show file classification |
 
@@ -130,15 +114,23 @@ Git pull  →  Decrypt  →  PathMapper  →  Merger  →  SecurityFilter  →
 | `claudefy machines` | List registered machines |
 | `claudefy restore` | Restore from a backup |
 | `claudefy doctor` | Diagnose sync health |
-| `claudefy config get/set` | View or update config |
+| `claudefy config get/set` | View or update config (with schema validation) |
+| `claudefy logs` | Show recent sync operations |
+| `claudefy export --output <path>` | Create a portable backup archive |
+| `claudefy rotate-passphrase` | Re-encrypt all files with a new passphrase |
+| `claudefy uninstall` | Remove claudefy hooks, config, and store |
+| `claudefy completion` | Output bash/zsh/fish shell completion scripts |
 
-### Global Options
+### Push/Pull Options
 
 | Option | Description |
 |--------|-------------|
 | `-q, --quiet` | Suppress output |
-| `--skip-encryption` | Skip encryption (testing only) |
+| `--skip-encryption` | Skip encryption (testing only, prints warning) |
 | `--skip-secret-scan` | Skip secret scanning on push |
+| `--dry-run` | Preview changes without writing |
+| `--only <item>` | Sync only a specific item (e.g., `--only commands`) |
+| `--force` | Push: skip pull-before-push step |
 
 ## Encryption
 
@@ -148,37 +140,37 @@ claudefy uses **AES-256-SIV** deterministic encryption via `@noble/ciphers`.
 - **JSONL files** — encrypted line-by-line, preserving git's ability to diff and merge individual lines.
 - **Other files** — encrypted as whole files.
 - **Key derivation** — PBKDF2-SHA256 with 600,000 iterations. Salt is derived from the backend URL, so SSH and HTTPS URLs for the same repo produce the same key.
-- **Reactive** — only files where the secret scanner detects a match are encrypted. Clean files stay in plaintext for easy inspection.
+
+### Encryption modes
+
+| Mode | Behavior |
+|------|----------|
+| `reactive` (default) | Only files where the secret scanner detects a match are encrypted. Unknown-tier files are always encrypted. Clean allowlisted files stay in plaintext. |
+| `full` | All files are encrypted regardless of scanner results. Maximum security, larger git diffs. |
+
+Set mode: `claudefy config set encryption.mode full`
 
 **Passphrase resolution order:**
 1. `CLAUDEFY_PASSPHRASE` environment variable (recommended)
 2. OS keychain (if configured)
 
-Interactive prompts only occur during `claudefy init` and `claudefy join` setup.
+Interactive prompts occur during `claudefy init`, `claudefy join`, `claudefy rotate-passphrase`, and `claudefy uninstall` (unless `--confirm` is passed).
 
 > See [docs/encryption.md](docs/encryption.md) for the full technical deep-dive.
 
 ## Security
 
-- `.credentials.json` is **never** synced (hardcoded deny).
+- `.credentials.json` and `settings.local.json` are **never** synced (hardcoded deny, cannot be overridden).
 - Remote `hooks`, `mcpServers`, `env`, `permissions`, `allowedTools`, and `apiKeyHelper` keys are **stripped** from settings.json on pull — prevents code injection from the remote.
-- Secret scanner checks 15 patterns (API keys, tokens, credentials) before push. Secrets trigger encryption; if encryption is disabled, the push is blocked.
-- Symlinks are validated against path traversal.
+- MCP server sync via `~/.claude.json` requires explicit opt-in (`syncMcpServers: true`). Server commands are validated for shell metacharacters and args are checked for injection patterns.
+- Path traversal protection on `@@HOME@@` sentinel expansion — resolved paths must stay within the home directory.
+- Secret scanner checks 15 built-in patterns (API keys, tokens, credentials) before push, plus user-defined custom patterns. Secrets trigger encryption; if encryption is disabled, the push is blocked.
+- Symlinks are skipped during sync and diff operations to prevent path traversal.
+- Concurrent operations are protected by a PID-based lockfile with 10-minute timeout.
 - Passphrases are never stored in plaintext on disk.
 
 > See [docs/security.md](docs/security.md) for the full security model.
 
-## Documentation
-
-| Document | Description |
-|----------|-------------|
-| [Architecture](docs/architecture.md) | System design, module map, data flows |
-| [Encryption](docs/encryption.md) | AES-SIV, PBKDF2, line-level encryption |
-| [Security](docs/security.md) | Threat model, hook stripping, secret scanning |
-| [Hooks & Auto-Sync](docs/hooks.md) | SessionStart/SessionEnd hooks, automatic sync |
-| [Override & Restore](docs/override-and-restore.md) | Override flow, backup system, restore |
-| [Path Mapping](docs/path-mapping.md) | Cross-machine path normalization |
-
 ## Configuration
 
 Config lives at `~/.claudefy/config.json`:
@@ -187,17 +179,40 @@ Config lives at `~/.claudefy/config.json`:
 {
   "version": 1,
   "backend": { "type": "git", "url": "git@github.com:you/claude-sync.git" },
-  "encryption": { "enabled": true, "useKeychain": false, "cacheDuration": "0" },
+  "encryption": { "enabled": true, "useKeychain": false, "cacheDuration": "0", "mode": "reactive" },
+  "claudeJson": { "sync": true, "syncMcpServers": false },
+  "secretScanner": { "customPatterns": [] },
+  "backups": { "maxCount": 10, "maxAgeDays": 30 },
   "machineId": "hostname-abc12345"
 }
 ```
 
+### Custom secret patterns
+
+Add patterns to detect organization-specific secrets:
+
+```bash
+claudefy config set secretScanner.customPatterns '[{"name":"Internal Token","regex":"MYCO_[A-Za-z0-9]{32}"}]'
+```
+
+## Documentation
+
+| Document | Description |
+|----------|-------------|
+| [Architecture](docs/architecture.md) | System design, module map, data flows |
+| [Encryption](docs/encryption.md) | AES-SIV, PBKDF2, line-level encryption |
+| [Security](docs/security.md) | Threat model, hook stripping, secret scanning |
+| [Hooks & Auto-Sync](docs/hooks.md) | SessionStart/SessionEnd hooks, automatic sync |
+| [Override & Restore](docs/override-and-restore.md) | Override flow, backup system, restore |
+| [Path Mapping](docs/path-mapping.md) | Cross-machine path normalization |
+
 ## Multi-Machine Workflow
 
 1. **First machine:** `claudefy init --backend <url> --hooks`
 2. **Other machines:** `claudefy join --backend <url> --hooks`
 3. **Auto-sync:** hooks handle push/pull at session boundaries
-4. **Override:** `claudefy override --confirm` when one machine should be the source of truth (other machines auto-detect and create a backup before applying)
+4. **Preview changes:** `claudefy diff` to see pending changes
+5. **Override:** `claudefy override --confirm` when one machine should be the source of truth (other machines auto-detect and create a backup before applying)
 
 ## Contributing
 

package/dist/claude-json-sync/claude-json-sync.js

@@ -1,5 +1,5 @@
 import { readFileSync, existsSync } from "node:fs";
-import { resolve } from "node:path";
+import { resolve, relative, isAbsolute } from "node:path";
 import { output } from "../output.js";
 const ALWAYS_SYNCABLE_KEYS = ["theme", "preferredNotifChannel"];
 const OPT_IN_SYNCABLE_KEYS = ["mcpServers"];
@@ -61,7 +61,7 @@ export class ClaudeJsonSync {
             const localServers = (local.mcpServers ?? {});
             const remoteServers = this.localizePaths(remote.mcpServers, options.homeDir);
             // Validate remote MCP server entries before merging
-            const shellMetacharPattern = /[;&|`$]/;
+            const shellMetacharPattern = /[;&|`$><\n\r(){}*\\]/;
             const validatedServers = {};
             for (const [name, cfg] of Object.entries(remoteServers)) {
                 const server = cfg;
@@ -69,6 +69,11 @@ export class ClaudeJsonSync {
                     output.warn(`Skipping remote MCP server "${name}": command contains shell metacharacters`);
                     continue;
                 }
+                // Reject commands where @@HOME@@ sentinel was not resolved (e.g. path traversal rejected)
+                if (typeof server.command === "string" && server.command.includes("@@HOME@@")) {
+                    output.warn(`Skipping remote MCP server "${name}": command contains unresolved path sentinel`);
+                    continue;
+                }
                 // Also validate args array entries for shell metacharacters
                 if (Array.isArray(server.args)) {
                     const unsafeArg = server.args.find((arg) => typeof arg === "string" && shellMetacharPattern.test(arg));
@@ -104,7 +109,8 @@ export class ClaudeJsonSync {
             const expanded = homeDir + obj.slice("@@HOME@@".length);
             const resolved = resolve(expanded);
             // Prevent path traversal — resolved path must stay within homeDir
-            if (!resolved.startsWith(homeDir + "/") && resolved !== homeDir) {
+            const rel = relative(homeDir, resolved);
+            if (rel && (rel.startsWith("..") || isAbsolute(rel))) {
                 output.warn(`Skipping unsafe @@HOME@@ path: ${obj}`);
                 return obj;
             }

package/dist/claude-json-sync/claude-json-sync.js.map

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package/dist/cli.js

@@ -95,7 +95,10 @@ program
 program
     .command("push")
     .description("Push local state to remote store")
-    .action(async function () {
+    .option("--only <item>", "Sync only this item")
+    .option("--force", "Skip pull-before-push")
+    .option("--dry-run", "Show what would change without writing")
+    .action(async function (options) {
     try {
         const global = await getGlobalOpts(this);
         const { PushCommand } = await import("./commands/push.js");
@@ -105,6 +108,9 @@ program
             skipEncryption: global.skipEncryption,
             skipSecretScan: global.skipSecretScan,
             passphrase: global.passphrase,
+            only: options.only,
+            force: options.force ?? false,
+            dryRun: options.dryRun ?? false,
         });
     }
     catch (err) {
@@ -115,7 +121,9 @@ program
 program
     .command("pull")
     .description("Pull remote state to local machine")
-    .action(async function () {
+    .option("--only <item>", "Sync only this item")
+    .option("--dry-run", "Show what would change without writing")
+    .action(async function (options) {
     try {
         const global = await getGlobalOpts(this);
         const { PullCommand } = await import("./commands/pull.js");
@@ -124,6 +132,8 @@ program
             quiet: global.quiet,
             skipEncryption: global.skipEncryption,
             passphrase: global.passphrase,
+            only: options.only,
+            dryRun: options.dryRun ?? false,
         });
     }
     catch (err) {
@@ -167,6 +177,29 @@ program
         process.exit(1);
     }
 });
+program
+    .command("diff")
+    .description("Preview what push or pull would change")
+    .option("--push", "Show only push-direction changes")
+    .option("--pull", "Show only pull-direction changes")
+    .action(async function (options) {
+    try {
+        const global = await getGlobalOpts(this);
+        const { DiffCommand } = await import("./commands/diff.js");
+        const cmd = new DiffCommand(homeDir);
+        await cmd.execute({
+            quiet: global.quiet,
+            skipEncryption: global.skipEncryption,
+            passphrase: global.passphrase,
+            push: options.push ?? false,
+            pull: options.pull ?? false,
+        });
+    }
+    catch (err) {
+        output.error(err instanceof Error ? err.message : String(err));
+        process.exit(1);
+    }
+});
 program
     .command("link <alias> <path>")
     .description("Map local path to canonical project ID")
@@ -241,6 +274,48 @@ program
         process.exit(1);
     }
 });
+program
+    .command("logs")
+    .description("Show recent sync operations")
+    .option("-n, --count <number>", "Number of entries to show", "10")
+    .action(async function (cmdOpts) {
+    try {
+        const global = await getGlobalOpts(this);
+        const { LogsCommand } = await import("./commands/logs.js");
+        const cmd = new LogsCommand(homeDir);
+        const count = parseInt(cmdOpts.count, 10);
+        if (!Number.isFinite(count) || count < 1) {
+            throw new Error(`Invalid count: "${cmdOpts.count}". Must be a positive number.`);
+        }
+        await cmd.execute({ ...global, count });
+    }
+    catch (err) {
+        output.error(err instanceof Error ? err.message : String(err));
+        process.exit(1);
+    }
+});
+program
+    .command("completion")
+    .description("Output shell completion script")
+    .option("--bash", "Output bash completion")
+    .option("--zsh", "Output zsh completion")
+    .option("--fish", "Output fish completion")
+    .action((cmdOpts) => {
+    const commands = program.commands.map((c) => c.name()).join(" ");
+    const commandList = program.commands.map((c) => c.name());
+    if (cmdOpts.fish) {
+        const fishCompletions = commandList
+            .map((c) => `complete -c claudefy -n '__fish_use_subcommand' -a '${c}'`)
+            .join("\n");
+        console.log(`# claudefy fish completion\n# Save to ~/.config/fish/completions/claudefy.fish\n\n${fishCompletions}`);
+    }
+    else if (cmdOpts.zsh) {
+        console.log(`# claudefy zsh completion\n# Add to your .zshrc:\n# eval "$(claudefy completion --zsh)"\n\n_claudefy() {\n  local commands="${commands}"\n  _arguments '1: :($commands)'\n}\ncompdef _claudefy claudefy`);
+    }
+    else {
+        console.log(`# claudefy bash completion\n# Add to your .bashrc:\n# eval "$(claudefy completion --bash)"\n\n_claudefy() {\n  local commands="${commands}"\n  COMPREPLY=($(compgen -W "$commands" -- "\${COMP_WORDS[COMP_CWORD]}"))\n}\ncomplete -F _claudefy claudefy`);
+    }
+});
 const configCmd = program.command("config").description("Manage claudefy configuration");
 configCmd
     .command("get [key]")
@@ -345,5 +420,55 @@ hooksCmd
         process.exit(1);
     }
 });
+program
+    .command("uninstall")
+    .description("Remove claudefy hooks, config, and store")
+    .option("--confirm", "Skip confirmation prompt")
+    .action(async function (options) {
+    try {
+        const global = await getGlobalOpts(this);
+        const { UninstallCommand } = await import("./commands/uninstall.js");
+        const cmd = new UninstallCommand(homeDir);
+        await cmd.execute({ quiet: global.quiet, confirm: options.confirm });
+    }
+    catch (err) {
+        output.error(err instanceof Error ? err.message : String(err));
+        process.exit(1);
+    }
+});
+program
+    .command("export")
+    .description("Create a portable backup archive")
+    .requiredOption("-o, --output <path>", "Output file path (e.g., ~/claude-backup.tar.gz)")
+    .action(async function (options) {
+    try {
+        const global = await getGlobalOpts(this);
+        const { ExportCommand } = await import("./commands/export.js");
+        const cmd = new ExportCommand(homeDir);
+        await cmd.execute({ quiet: global.quiet, output: options.output });
+    }
+    catch (err) {
+        output.error(err instanceof Error ? err.message : String(err));
+        process.exit(1);
+    }
+});
+program
+    .command("rotate-passphrase")
+    .description("Re-encrypt all files with a new passphrase")
+    .action(async function () {
+    try {
+        const global = await getGlobalOpts(this);
+        const { RotatePassphraseCommand } = await import("./commands/rotate-passphrase.js");
+        const cmd = new RotatePassphraseCommand(homeDir);
+        await cmd.execute({
+            quiet: global.quiet,
+            oldPassphrase: global.passphrase,
+        });
+    }
+    catch (err) {
+        output.error(err instanceof Error ? err.message : String(err));
+        process.exit(1);
+    }
+});
 export { program };
 //# sourceMappingURL=cli.js.map

package/dist/cli.js.map

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package/dist/commands/config.d.ts

@@ -1,5 +1,6 @@
 export declare class ConfigCommand {
     private homeDir;
+    private static readonly CONFIG_SCHEMA;
     constructor(homeDir: string);
     get(key?: string): Promise<unknown>;
     private static readonly FORBIDDEN_KEYS;

package/dist/commands/config.js

@@ -1,6 +1,21 @@
 import { ConfigManager } from "../config/config-manager.js";
+import { output } from "../output.js";
 export class ConfigCommand {
     homeDir;
+    static CONFIG_SCHEMA = {
+        "encryption.enabled": { type: "boolean" },
+        "encryption.useKeychain": { type: "boolean" },
+        "encryption.cacheDuration": { type: "string" },
+        "encryption.mode": { type: "string", values: ["reactive", "full"] },
+        "backend.type": { type: "string", values: ["git"] },
+        "backend.url": { type: "string" },
+        "claudeJson.sync": { type: "boolean" },
+        "claudeJson.syncMcpServers": { type: "boolean" },
+        "secretScanner.customPatterns": { type: "object" },
+        "backups.maxCount": { type: "number" },
+        "backups.maxAgeDays": { type: "number" },
+        version: { type: "number" },
+    };
     constructor(homeDir) {
         this.homeDir = homeDir;
     }
@@ -37,12 +52,37 @@ export class ConfigCommand {
                 throw new Error(`Invalid config key: "${key}" — "${part}" is not allowed`);
             }
         }
-        const parsed = this.parseValue(value);
+        const schema = ConfigCommand.CONFIG_SCHEMA[key];
+        const parsed = this.parseValue(value, schema?.type);
+        if (schema) {
+            const actualType = typeof parsed;
+            if (actualType !== schema.type && !(schema.type === "object" && Array.isArray(parsed))) {
+                throw new Error(`"${key}" expects ${schema.type}, got ${actualType}`);
+            }
+            if (schema.values && !schema.values.includes(parsed)) {
+                throw new Error(`"${key}" must be one of: ${schema.values.join(", ")}`);
+            }
+        }
+        else {
+            output.warn(`Unknown config key "${key}". Setting anyway.`);
+        }
         await configManager.set(key, parsed);
     }
-    parseValue(value) {
+    parseValue(value, schemaType) {
         if (typeof value !== "string")
             return value;
+        // If schema says string, don't coerce
+        if (schemaType === "string")
+            return value;
+        // If schema says object, try JSON parsing
+        if (schemaType === "object") {
+            try {
+                return JSON.parse(value);
+            }
+            catch {
+                throw new Error(`Expected JSON for object value, got: ${value}`);
+            }
+        }
         if (value === "true")
             return true;
         if (value === "false")

package/dist/commands/config.js.map

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package/dist/commands/diff.d.ts

@@ -0,0 +1,28 @@
+import type { DiffResult } from "../diff-utils/diff-utils.js";
+export interface DiffOptions {
+    quiet: boolean;
+    push?: boolean;
+    pull?: boolean;
+    skipEncryption?: boolean;
+    passphrase?: string;
+}
+interface DirectionResult {
+    direction: "push" | "pull";
+    diff: DiffResult;
+}
+export declare class DiffCommand {
+    private readonly homeDir;
+    private readonly claudeDir;
+    private readonly configManager;
+    constructor(homeDir: string);
+    execute(options: DiffOptions): Promise<DirectionResult[]>;
+    /**
+     * Compute pull diff, handling .age files by stripping the .age suffix
+     * and replacing their content with a placeholder so encrypted files
+     * can be compared by logical name against local unencrypted files.
+     */
+    private computePullDiff;
+    private stripAgeExtensions;
+    private printResults;
+}
+export {};