refactor: remove MA_COMMAND env var, use --command flag only

Command resolution is now simpler and safer:
1. --command / -c flag
2. Filename pattern (task.claude.md → claude)

Removes risk of forgotten env vars causing unexpected behavior.

Author: johnlindquist

README.md

@@ -99,8 +99,9 @@ bun install && bun link
 ma task.claude.md
 ma task.gemini.md
 
-# Override command via environment variable
-MA_COMMAND=claude ma task.md
+# Override command via --command flag
+ma task.md --command claude
+ma task.md -c gemini
 
 # Pass additional flags to the command
 ma task.claude.md --verbose --debug
@@ -115,8 +116,7 @@ ma task.claude.md --verbose --debug
 Commands are resolved in this priority order:
 
 1. **CLI flag**: `--command claude` or `-c claude`
-2. **Environment variable**: `MA_COMMAND=claude`
-3. **Filename pattern**: `task.claude.md` → `claude`
+2. **Filename pattern**: `task.claude.md` → `claude`
 
 If no command can be resolved, you'll get an error with instructions.
 
@@ -426,8 +426,7 @@ Usage: ma <file.md> [any flags for the command]
 
 Command resolution:
   1. --command flag (e.g., ma task.md --command claude)
-  2. MA_COMMAND env var (e.g., MA_COMMAND=claude ma task.md)
-  3. Filename pattern (e.g., task.claude.md → 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
@@ -438,7 +437,6 @@ Examples:
   ma commit.gemini.md
   ma task.md --command claude
   ma task.md -c gemini
-  MA_COMMAND=claude ma task.md
 
 Without a file:
   ma --setup    Configure shell to run .md files directly
@@ -450,7 +448,6 @@ Without a file:
 
 | Variable | Description |
 |----------|-------------|
-| `MA_COMMAND` | Override command (e.g., `MA_COMMAND=claude ma task.md`) |
 | `MA_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`) |
 

src/cli.ts

@@ -58,12 +58,13 @@ export function parseCliArgs(argv: string[]): CliArgs {
 function printHelp() {
   console.log(`
 Usage: ma <file.md> [any flags for the command]
+       ma <file.md> --command <cmd>
        ma --setup
        ma --logs
        ma --help
 
 Command resolution:
-  1. MA_COMMAND env var (e.g., MA_COMMAND=claude ma task.md)
+  1. --command flag (e.g., ma task.md --command claude)
   2. Filename pattern (e.g., task.claude.md → claude)
 
 All frontmatter keys are passed as CLI flags to the command.
@@ -73,7 +74,8 @@ Examples:
   ma task.claude.md -p "print mode"
   ma task.claude.md --model opus --verbose
   ma commit.gemini.md
-  MA_COMMAND=claude ma task.md
+  ma task.md --command claude
+  ma task.md -c gemini
 
 Config file example (~/.markdown-agent/config.yaml):
   commands:

src/command.test.ts

@@ -1,4 +1,4 @@
-import { expect, test, describe, beforeEach, afterEach } from "bun:test";
+import { expect, test, describe } from "bun:test";
 import { parseCommandFromFilename, resolveCommand, buildArgs, extractPositionalMappings, extractEnvVars } from "./command";
 
 describe("parseCommandFromFilename", () => {
@@ -25,29 +25,9 @@ describe("parseCommandFromFilename", () => {
 });
 
 describe("resolveCommand", () => {
-  const originalEnv = process.env.MA_COMMAND;
-
-  beforeEach(() => {
-    delete process.env.MA_COMMAND;
-  });
-
-  afterEach(() => {
-    if (originalEnv !== undefined) {
-      process.env.MA_COMMAND = originalEnv;
-    } else {
-      delete process.env.MA_COMMAND;
-    }
-  });
-
-  test("MA_COMMAND env var takes priority over filename", () => {
-    process.env.MA_COMMAND = "gemini";
-    const result = resolveCommand("task.claude.md");
-    expect(result).toBe("gemini");
-  });
-
-  test("filename inference works when no env var", () => {
-    const result = resolveCommand("task.claude.md");
-    expect(result).toBe("claude");
+  test("resolves command from filename pattern", () => {
+    expect(resolveCommand("task.claude.md")).toBe("claude");
+    expect(resolveCommand("review.gemini.md")).toBe("gemini");
   });
 
   test("throws when no command can be resolved", () => {

src/command.ts

@@ -36,25 +36,17 @@ export function parseCommandFromFilename(filePath: string): string | undefined {
 }
 
 /**
- * Resolve which command to use
- * Priority: MA_COMMAND env var > filename inference
+ * Resolve command from filename pattern
+ * Note: --command flag is handled in index.ts before this is called
  */
 export function resolveCommand(filePath: string): string {
-  // 1. MA_COMMAND environment variable
-  const fromEnv = process.env.MA_COMMAND;
-  if (fromEnv) {
-    return fromEnv;
-  }
-
-  // 2. Infer from filename
   const fromFilename = parseCommandFromFilename(filePath);
   if (fromFilename) {
     return fromFilename;
   }
 
-  // 3. No command specified - error
   throw new Error(
-    "No command specified. Set MA_COMMAND env var, " +
+    "No command specified. Use --command flag, " +
     "or name your file like 'task.claude.md'"
   );
 }