refactor: rename markdown-agent to mdflow

- Package name: markdown-agent → mdflow
- CLI commands: ma → md (and mdflow)
- Config directory: ~/.markdown-agent → ~/.mdflow
- Project config files: ma.config.yaml → mdflow.config.yaml
- Agent directories: .ma/ → .mdflow/, ~/.ma/ → ~/.mdflow/
- Log directory: ~/.mdflow/logs
- Known hosts: ~/.mdflow/known_hosts
- Updated all tests to use new naming

Author: johnlindquist

.cursor/rules/use-bun-instead-of-node-vite-npm-pnpm.mdc

@@ -26,11 +26,14 @@ report.[0-9]_.[0-9]_.[0-9]_.[0-9]_.json
 .eslintcache
 .cache
 *.tsbuildinfo
-.markdown-agent
+.mdflow
 
 # IntelliJ based IDEs
 .idea
 
+# Cursor
+.cursor/
+
 # Finder (MacOS) folder config
 .DS_Store
 PRESENTATION.md

.gitignore

@@ -13,23 +13,6 @@
     "editor.findMatchHighlightBorder": "#ffffff",
     "editor.findMatchHighlightBackground": "#000000ee",
     "editor.findMatchHighlightForeground": "#ffffffee",
-    "activityBar.background": "#211C7F",
-    "activityBar.activeBackground": "#211C7F",
-    "activityBar.activeBorder": "#797F1C",
-    "activityBar.foreground": "#FCFCFE",
-    "activityBar.inactiveForeground": "#FCFCFE99",
-    "activityBarBadge.background": "#797F1C",
-    "activityBarBadge.foreground": "#FCFCFE",
-    "titleBar.activeBackground": "#2E27B1",
-    "titleBar.activeForeground": "#FCFCFE",
-    "titleBar.inactiveBackground": "#2E27B199",
-    "titleBar.inactiveForeground": "#FCFCFE99",
-    "sash.hoverBorder": "#211C7F",
-    "commandCenter.border": "#FCFCFE99",
-    "statusBar.background": "#2E27B1",
-    "statusBar.foreground": "#FCFCFE",
-    "statusBarItem.hoverBackground": "#2A23A0",
-    "statusBarItem.remoteBackground": "#2E27B1",
-    "statusBarItem.remoteForeground": "#FCFCFE"
+    "activityBar.activeBorder": "#797F1C"
   }
 }

.vscode/settings.json

@@ -4,16 +4,16 @@ This file provides guidance to Claude Code (claude.ai/code) when working with co
 
 ## Overview
 
-**markdown-agent** (`ma`) is a CLI tool that executes AI agents defined as markdown files. It parses YAML frontmatter for configuration and passes keys directly as CLI flags to the specified command (claude, codex, gemini, copilot, or any other CLI tool).
+**mdflow** (`md`) is a CLI tool that executes AI agents defined as markdown files. It parses YAML frontmatter for configuration and passes keys directly as CLI flags to the specified command (claude, codex, gemini, copilot, or any other CLI tool).
 
 ## CLI Subcommands
 
 ```bash
-ma <file.md> [flags]     # Run an agent
-ma create [name]         # Create a new agent file
-ma setup                 # Configure shell (PATH, aliases)
-ma logs                  # Show agent log directory
-ma help                  # Show help
+md <file.md> [flags]     # Run an agent
+md create [name]         # Create a new agent file
+md setup                 # Configure shell (PATH, aliases)
+md logs                  # Show agent log directory
+md help                  # Show help
 ```
 
 ## Development Commands
@@ -32,7 +32,7 @@ bun test --test-name-pattern "parses command"
 bun run src/index.ts task.claude.md
 
 # Or using the alias
-bun run ma task.claude.md
+bun run md task.claude.md
 ```
 
 ## Architecture
@@ -56,7 +56,7 @@ bun run ma task.claude.md
   - `runCommand()`: Spawns the command with positional args
 
 - **`config.ts`** - Global configuration
-  - Loads defaults from `~/.markdown-agent/config.yaml`
+  - Loads defaults from `~/.mdflow/config.yaml`
   - Built-in defaults: All commands default to print mode
   - `getCommandDefaults()`: Get defaults for a command
   - `applyDefaults()`: Merge defaults with frontmatter
@@ -80,7 +80,7 @@ bun run ma task.claude.md
 
 - **`template.ts`** - LiquidJS-powered template engine for variable substitution
 
-- **`logger.ts`** - Structured logging with pino (logs to `~/.markdown-agent/logs/<agent>/`)
+- **`logger.ts`** - Structured logging with pino (logs to `~/.mdflow/logs/<agent>/`)
 
 ### Command Resolution
 
@@ -90,7 +90,7 @@ Commands are resolved in priority order:
 
 ### Frontmatter Keys
 
-**System keys** (consumed by ma, not passed to command):
+**System keys** (consumed by md, not passed to command):
 - `args`: Named positional arguments for template vars
 - `env` (object form): Sets process.env before execution
 - `$1`, `$2`, etc.: Map positional args to flags
@@ -137,7 +137,7 @@ task.gemini.md      # Print mode: gemini "..." (one-shot)
 task.i.gemini.md    # Interactive: gemini --prompt-interactive "..."
 ```
 
-### Global Config (`~/.markdown-agent/config.yaml`)
+### Global Config (`~/.mdflow/config.yaml`)
 
 Set default frontmatter per command:
 

CLAUDE.md

@@ -1,4 +1,4 @@
-# markdown-agent
+# mdflow
 
 ```bash
 review.claude.md                 # Run with Claude
@@ -67,7 +67,7 @@ The markdown body is passed as the final argument to the command.
 
 ## Unix Philosophy
 
-markdown-agent embraces the Unix philosophy:
+mdflow embraces the Unix philosophy:
 
 - **No magic mapping** - Frontmatter keys pass directly to the command
 - **Stdin/stdout** - Pipe data in and out
@@ -76,18 +76,18 @@ markdown-agent embraces the Unix philosophy:
 
 ```bash
 # Pipe input
-git diff | ma review.claude.md
+git diff | mdflow review.claude.md
 
 # Chain agents
-ma plan.claude.md | ma implement.codex.md
+mdflow plan.claude.md | mdflow implement.codex.md
 ```
 
 ---
 
 ## Installation
 
 ```bash
-npm install -g markdown-agent
+npm install -g mdflow
 # or
 bun install && bun link
 ```
@@ -96,18 +96,18 @@ bun install && bun link
 
 ```bash
 # Run with filename-inferred command
-ma task.claude.md
-ma task.gemini.md
+mdflow task.claude.md
+mdflow task.gemini.md
 
 # Override command via --command flag
-ma task.md --command claude
-ma task.md -c gemini
+mdflow task.md --command claude
+mdflow task.md -c gemini
 
 # Pass additional flags to the command
-ma task.claude.md --verbose --debug
+mdflow task.claude.md --verbose --debug
 ```
 
-> **Note:** Both `ma` and `markdown-agent` commands are available.
+> **Note:** Both `mdflow` and `md` commands are available.
 
 ---
 
@@ -124,19 +124,19 @@ If no command can be resolved, you'll get an error with instructions.
 
 ## Flag Hijacking
 
-Some CLI flags are "hijacked" by markdown-agent—they're consumed and never passed to the underlying command. This allows generic markdown files without command names to be executed.
+Some CLI flags are "hijacked" by mdflow—they're consumed and never passed to the underlying command. This allows generic markdown files without command names to be executed.
 
 ### `--command` / `-c`
 
 Override the command for any markdown file:
 
 ```bash
 # Run a generic .md file with any command
-ma task.md --command claude
-ma task.md -c gemini
+mdflow task.md --command claude
+mdflow task.md -c gemini
 
 # Override the filename-inferred command
-ma task.claude.md --command gemini  # Runs gemini, not claude
+mdflow task.claude.md --command gemini  # Runs gemini, not claude
 ```
 
 ### `$varname` Fields
@@ -153,19 +153,19 @@ Build {{ feature_name }} in {{ target_dir }}.
 
 ```bash
 # Use defaults
-ma create.claude.md
+mdflow create.claude.md
 
 # Override with CLI flags (hijacked, not passed to command)
-ma create.claude.md --feature_name "Payments" --target_dir "src/billing"
+mdflow create.claude.md --feature_name "Payments" --target_dir "src/billing"
 ```
 
-The `--feature_name` and `--target_dir` flags are consumed by markdown-agent for template substitution—they won't be passed to the command.
+The `--feature_name` and `--target_dir` flags are consumed by mdflow for template substitution—they won't be passed to the command.
 
 ---
 
 ## Frontmatter Reference
 
-### System Keys (handled by markdown-agent)
+### System Keys (handled by mdflow)
 
 | Field | Type | Description |
 |-------|------|-------------|
@@ -234,15 +234,15 @@ Review this code with me interactively.
 Or use CLI flags:
 
 ```bash
-ma task.claude.md --_interactive  # Enable interactive mode
-ma task.claude.md -_i             # Short form
+mdflow task.claude.md --_interactive  # Enable interactive mode
+mdflow task.claude.md -_i             # Short form
 ```
 
 ---
 
 ## Global Configuration
 
-Set default frontmatter per command in `~/.markdown-agent/config.yaml`:
+Set default frontmatter per command in `~/.mdflow/config.yaml`:
 
 ```yaml
 commands:
@@ -323,7 +323,7 @@ Create a new feature called "{{ feature_name }}" in {{ target_dir }}.
 ```
 
 ```bash
-ma create-feature.claude.md "Auth" "src/features"
+mdflow create-feature.claude.md "Auth" "src/features"
 ```
 
 ### Environment Variables
@@ -378,7 +378,7 @@ Glob imports:
 - Respect `.gitignore` automatically
 - Include common exclusions (`node_modules`, `.git`, etc.)
 - Are limited to ~100,000 tokens by default
-- Set `MA_FORCE_CONTEXT=1` to override the token limit
+- Set `MDFLOW_FORCE_CONTEXT=1` to override the token limit
 
 Files are formatted as XML with path attributes:
 
@@ -443,7 +443,7 @@ Fetch content from URLs (markdown and JSON only):
 
 ## Environment Variables
 
-markdown-agent automatically loads `.env` files from the markdown file's directory.
+mdflow automatically loads `.env` files from the markdown file's directory.
 
 ### Loading Order
 
@@ -472,43 +472,43 @@ Environment variables are available:
 ## CLI Options
 
 ```
-Usage: ma <file.md> [any flags for the command]
-       ma <file.md> --command <cmd>
-       ma --setup
-       ma --logs
-       ma --help
+Usage: mdflow <file.md> [any flags for the command]
+       mdflow <file.md> --command <cmd>
+       mdflow --setup
+       mdflow --logs
+       mdflow --help
 
 Command resolution:
-  1. --command flag (e.g., ma task.md --command claude)
+  1. --command flag (e.g., mdflow task.md --command claude)
   2. Filename pattern (e.g., task.claude.md → claude)
 
 All frontmatter keys are passed as CLI flags to the command.
-Global defaults can be set in ~/.markdown-agent/config.yaml
+Global defaults can be set in ~/.mdflow/config.yaml
 
-ma-specific flags (consumed, not passed to command):
+mdflow-specific flags (consumed, not passed to command):
   --command, -c       Specify command to run
   --dry-run           Preview without executing
   --_interactive, -_i Enable interactive mode
 
 Examples:
-  ma task.claude.md -p "print mode"
-  ma task.claude.md --model opus --verbose
-  ma commit.gemini.md
-  ma task.md --command claude
-  ma task.md -c gemini
-  ma task.claude.md -_i  # Run in interactive mode
+  mdflow task.claude.md -p "print mode"
+  mdflow task.claude.md --model opus --verbose
+  mdflow commit.gemini.md
+  mdflow task.md --command claude
+  mdflow task.md -c gemini
+  mdflow task.claude.md -_i  # Run in interactive mode
 
 Without a file:
-  ma --setup    Configure shell to run .md files directly
-  ma --logs     Show log directory
-  ma --help     Show this help
+  mdflow --setup    Configure shell to run .md files directly
+  mdflow --logs     Show log directory
+  mdflow --help     Show this help
 ```
 
 ### Environment Variables
 
 | Variable | Description |
 |----------|-------------|
-| `MA_FORCE_CONTEXT` | Set to `1` to disable the 100k token limit for glob imports |
+| `MDFLOW_FORCE_CONTEXT` | Set to `1` to disable the 100k token limit for glob imports |
 | `NODE_ENV` | Controls which `.env.[NODE_ENV]` file is loaded (default: `development`) |
 
 ---
@@ -518,7 +518,7 @@ Without a file:
 Make `.md` files directly executable:
 
 ```bash
-ma --setup   # One-time setup
+mdflow --setup   # One-time setup
 ```
 
 Then run agents directly:
@@ -533,7 +533,7 @@ task.claude.md --verbose         # With passthrough args
 Add to `~/.zshrc`:
 
 ```bash
-alias -s md='ma'
+alias -s md='mdflow'
 export PATH="$HOME/agents:$PATH"  # Your agent library
 ```
 
@@ -570,6 +570,6 @@ git diff | review.claude.md      # Review staged changes
 
 - If no frontmatter is present, the file is printed as-is (unless command inferred from filename)
 - Template system uses [LiquidJS](https://liquidjs.com/) - supports conditionals, loops, and filters
-- Logs are always written to `~/.markdown-agent/logs/<agent-name>/` for debugging
+- Logs are always written to `~/.mdflow/logs/<agent-name>/` for debugging
 - Use `--logs` to show the log directory
 - Stdin is wrapped in `<stdin>` tags and prepended to the prompt

README.md

@@ -1,5 +1,5 @@
 {
-  "name": "markdown-agent",
+  "name": "mdflow",
   "version": "2.16.0",
   "module": "src/index.ts",
   "type": "module",
@@ -8,12 +8,12 @@
     "url": "https://github.com/johnlindquist/markdown-agent.git"
   },
   "bin": {
-    "markdown-agent": "./src/index.ts",
-    "ma": "./src/index.ts"
+    "mdflow": "./src/index.ts",
+    "md": "./src/index.ts"
   },
   "scripts": {
     "test": "bun test --bail=1",
-    "ma": "bun run src/index.ts"
+    "md": "bun run src/index.ts"
   },
   "devDependencies": {
     "@semantic-release/changelog": "^6.0.3",