fix: environment variables now correctly take precedence over config file values

The README documented that environment variables take precedence over
config file values, but the code had the opposite behavior. This fix
corrects the precedence order in getRawOption to match the documentation:

1. CLI flags (highest priority)
2. Environment variables
3. Config file (lowest priority)

Also adds subprocess-based tests that verify:
- Env vars win when both env var and config file are present
- Config file is used as fallback when no env var is set

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

Author: 2 people

CHANGELOG.md

@@ -2,6 +2,10 @@
 
 ## [Unreleased]
 
+### Fixed
+
+- environment variables now correctly take precedence over config file values
+
 ## [1.6.0] - 2026-01-05
 
 ### Added

src/config.ts

@@ -108,8 +108,9 @@ export type Options = v.InferOutput<typeof OptionsSchema>
 export type OptionName = keyof Options
 
 function getRawOption(optionName: OptionName, cliValue?: string): unknown {
-  return cliValue ?? config[optionName] ??
-    Deno.env.get("LINEAR_" + optionName.toUpperCase())
+  return cliValue ??
+    Deno.env.get("LINEAR_" + optionName.toUpperCase()) ??
+    config[optionName]
 }
 
 export function getOption<T extends OptionName>(

test/config.test.ts

@@ -52,3 +52,105 @@ Deno.test("getOption - download_images returns undefined for unrecognized string
   const result = getOption("download_images", "maybe")
   assertEquals(result, undefined)
 })
+
+Deno.test("getOption - environment variables take precedence over config file", async () => {
+  // Create a temp directory with a config file
+  const tempDir = await Deno.makeTempDir()
+  const configValue = "from-config-file"
+  const envValue = "from-env-var"
+
+  try {
+    // Write a .linear.toml with a workspace value
+    await Deno.writeTextFile(
+      `${tempDir}/.linear.toml`,
+      `workspace = "${configValue}"\n`,
+    )
+
+    // Get absolute paths to the config module and deno.json
+    const configPath = new URL("../src/config.ts", import.meta.url).pathname
+    const denoJsonPath = new URL("../deno.json", import.meta.url).pathname
+
+    // Run a subprocess that imports config and prints the workspace value
+    // The subprocess runs from the temp directory so it loads our test config
+    const command = new Deno.Command("deno", {
+      args: [
+        "eval",
+        `--config=${denoJsonPath}`,
+        `import { getOption } from "file://${configPath}"; console.log(getOption("workspace") ?? "undefined");`,
+      ],
+      cwd: tempDir,
+      env: {
+        LINEAR_WORKSPACE: envValue,
+      },
+      stdout: "piped",
+      stderr: "piped",
+    })
+
+    const { stdout, stderr } = await command.output()
+    const output = new TextDecoder().decode(stdout).trim()
+    const errorOutput = new TextDecoder().decode(stderr)
+
+    if (errorOutput) {
+      console.error("Subprocess stderr:", errorOutput)
+    }
+
+    // The env var should win over the config file
+    assertEquals(
+      output,
+      envValue,
+      "Environment variable should take precedence over config file",
+    )
+  } finally {
+    // Clean up temp directory
+    await Deno.remove(tempDir, { recursive: true })
+  }
+})
+
+Deno.test("getOption - config file is used when no env var is set", async () => {
+  // Create a temp directory with a config file
+  const tempDir = await Deno.makeTempDir()
+  const configValue = "from-config-file"
+
+  try {
+    // Write a .linear.toml with a workspace value
+    await Deno.writeTextFile(
+      `${tempDir}/.linear.toml`,
+      `workspace = "${configValue}"\n`,
+    )
+
+    // Get absolute paths to the config module and deno.json
+    const configPath = new URL("../src/config.ts", import.meta.url).pathname
+    const denoJsonPath = new URL("../deno.json", import.meta.url).pathname
+
+    // Run a subprocess without LINEAR_WORKSPACE env var
+    const command = new Deno.Command("deno", {
+      args: [
+        "eval",
+        `--config=${denoJsonPath}`,
+        `import { getOption } from "file://${configPath}"; console.log(getOption("workspace") ?? "undefined");`,
+      ],
+      cwd: tempDir,
+      env: {}, // No LINEAR_WORKSPACE set
+      stdout: "piped",
+      stderr: "piped",
+    })
+
+    const { stdout, stderr } = await command.output()
+    const output = new TextDecoder().decode(stdout).trim()
+    const errorOutput = new TextDecoder().decode(stderr)
+
+    if (errorOutput) {
+      console.error("Subprocess stderr:", errorOutput)
+    }
+
+    // The config file value should be used as fallback
+    assertEquals(
+      output,
+      configValue,
+      "Config file should be used when no env var is set",
+    )
+  } finally {
+    // Clean up temp directory
+    await Deno.remove(tempDir, { recursive: true })
+  }
+})