fix(workspace): preserve existing CLAUDE.md and AGENTS.md on init (#63)

* fix(workspace): preserve existing CLAUDE.md and AGENTS.md on init

When running `workspace init`, skip copying agent files from the
template source if they already exist in the target directory. Existing
files still receive WORKSPACE-RULES injection (append) without losing
user content.

Closes #62

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

* fix(test): run non-workspace e2e tests from temp cwd

Tests asserting "non-workspace dir" behavior were inheriting the test
runner's cwd which may contain .allagents/workspace.yaml, causing the
"No plugins configured" path to be skipped. Set cwd to the temp
directory so tests are isolated from the project's own workspace config.

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

* test(e2e): verify workspace init preserves existing CLAUDE.md and AGENTS.md

Runs the built CLI binary with `workspace init --from` against a
directory that already has CLAUDE.md/AGENTS.md and asserts the
original content is preserved while WORKSPACE-RULES are appended.

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

* revert: remove redundant e2e test for workspace init

The unit test in workspace-init-preserve.test.ts already calls
initWorkspace() directly and covers the same code path without
requiring a pre-built binary.

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

* chore(test): remove e2e tests that require pre-built binary

These tests spawned `node dist/index.js` and required a build step
before running. They were also brittle (cwd leaked project state into
"non-workspace" assertions). Remove them; the enriched-help and
metadata tests in tests/unit/ and tests/e2e/cli-enriched-help.test.ts
cover the same logic by importing source directly.

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

* test(unit): add unit tests for agent-help and json-output modules

Replace removed e2e binary-spawning tests with unit tests that import
source directly:
- agent-help: flag extraction, command metadata completeness, options/positionals
- json-output: flag extraction and position flexibility

The --help output tests are not replaced since they tested cmd-ts
framework behavior, not our code. cli-enriched-help.test.ts already
covers our metadata structure.

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

---------

Co-authored-by: Claude Opus 4.5 <noreply@anthropic.com>

Author: christso

src/core/workspace.ts

@@ -182,6 +182,12 @@ export async function initWorkspace(
       if (parsedUrl) {
         const basePath = parsedUrl.subpath || '';
         for (const agentFile of AGENT_FILES) {
+          const targetFilePath = join(absoluteTarget, agentFile);
+          // Skip if file already exists in target - don't overwrite user content
+          if (existsSync(targetFilePath)) {
+            copiedAgentFiles.push(agentFile);
+            continue;
+          }
           const filePath = basePath ? `${basePath}/${agentFile}` : agentFile;
           const content = await fetchFileFromGitHub(
             parsedUrl.owner,
@@ -190,7 +196,7 @@ export async function initWorkspace(
             parsedUrl.branch,
           );
           if (content) {
-            await writeFile(join(absoluteTarget, agentFile), content, 'utf-8');
+            await writeFile(targetFilePath, content, 'utf-8');
             copiedAgentFiles.push(agentFile);
           }
         }
@@ -199,10 +205,16 @@ export async function initWorkspace(
       // Copy agent files from local source
       const effectiveSourceDir = sourceDir ?? defaultTemplatePath;
       for (const agentFile of AGENT_FILES) {
+        const targetFilePath = join(absoluteTarget, agentFile);
+        // Skip if file already exists in target - don't overwrite user content
+        if (existsSync(targetFilePath)) {
+          copiedAgentFiles.push(agentFile);
+          continue;
+        }
         const sourcePath = join(effectiveSourceDir, agentFile);
         if (existsSync(sourcePath)) {
           const content = await readFile(sourcePath, 'utf-8');
-          await writeFile(join(absoluteTarget, agentFile), content, 'utf-8');
+          await writeFile(targetFilePath, content, 'utf-8');
           copiedAgentFiles.push(agentFile);
         }
       }