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diff --git a/‎packages/cli/src/commands/workflow.test.ts‎
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diff --git a/‎packages/cli/src/commands/workflow.ts‎
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@@ -32,6 +32,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - **`archon setup` no longer writes to `<repo>/.env`.** Prior versions unconditionally wrote the generated config to both `~/.archon/.env` and `<repo>/.env`, destroying user-added secrets and silently downgrading PostgreSQL configs to SQLite when re-run in "Add" mode. The write side now targets exactly one archon-owned file (home or project scope via `--scope`), merges into existing content by default, and writes a timestamped backup. `<repo>/.env` is never touched — it belongs to the user's target project. (#1303)
 - **CLI and server no longer silently lose repo-local env vars.** Previously, env vars in `<repo>/.env` were parsed, deleted from `process.env` by `stripCwdEnv()`, and the only output operators saw was `[dotenv@17.3.1] injecting env (0) from .env` — which read as "file was empty." Workflows that needed `SLACK_WEBHOOK` or similar had no way to recover without knowing to use `~/.archon/.env`. The new `<cwd>/.archon/.env` path + archon-owned log lines make the load state observable and recoverable. (#1302)
 - **Bumped transitive `axios` to `^1.15.0` via root `overrides` to clear CVE-2025-62718** (NO_PROXY bypass via hostname normalization → potential SSRF). Archon pulls `axios` transitively through `@slack/bolt` and `@slack/web-api`; both semver ranges (`^1.12.0` and `^1.13.5`) accept the override cleanly, so no API surface changes. Credits @stefans71 for identifying and reporting the vulnerability in #1153. Closes #1053.
+- **Stale workspace symlink no longer reported as "not in a git repository" by the CLI.** When `archon workflow run` (or `--resume`) is invoked from a valid git repo whose `~/.archon/workspaces/<owner>/<repo>/source` symlink points somewhere else (common after moving/renaming the checkout), auto-registration fails but the repo is fine. Previously both the worktree-creation and resume paths fell through to the generic `Cannot create worktree: not in a git repository` / `Cannot resume: Not in a git repository` errors — a lie that sent users down the wrong diagnostic path. Both sites now preserve the registration error and throw `Cannot {create worktree,resume}: repository registration failed.` with the original cause and a concrete cleanup hint (`Remove the stale workspace entry at <path> and retry`) when the failure matches the `createProjectSourceSymlink()` shape. Credits @Bortlesboat for identifying the root cause and the parser approach in #1157. Closes #1146.
 
 - **Server startup no longer marks actively-running workflows as failed.** The `failOrphanedRuns()` call has been removed from `packages/server/src/index.ts` to match the CLI precedent (`packages/cli/src/cli.ts:256-258`). Per the new CLAUDE.md principle "No Autonomous Lifecycle Mutation Across Process Boundaries", a stuck `running` row is now transitioned explicitly by the user: via the per-row Cancel/Abandon buttons on the dashboard workflow card, or `archon workflow abandon <run-id>` from the CLI. (`archon workflow cleanup` is a separate command that deletes OLD terminal runs for disk hygiene — it does not handle stuck `running` rows.) Closes #1216.
 - **`MCP server connection failed: <plugin>` noise no longer surfaces in workflow runs.** The dag-executor now loads the workflow node's `mcp:` config file once and filters the SDK's failure message to only the servers the workflow actually configured. User-level Claude plugin MCPs (e.g. `telegram` inherited from `~/.claude/`) that fail to connect in the headless subprocess are debug-logged as `dag.mcp_plugin_connection_suppressed` instead of being forwarded to the conversation. Other provider warnings (⚠️) surface unchanged. Credits @MrFadiAi for reporting the issue in #1134 (that PR was 9 days stale and conflicting; this is a fresh re-do on current `dev`).
 
@@ -865,6 +865,114 @@ describe('workflowRunCommand', () => {
     expect(createCallsAfter).toBe(createCallsBefore);
   });
 
+  // -------------------------------------------------------------------------
+  // Stale workspace source-symlink → truthful CLI error
+  // -------------------------------------------------------------------------
+
+  it('surfaces auto-registration failures instead of claiming the repo is invalid', async () => {
+    const { discoverWorkflowsWithConfig } = await import('@archon/workflows/workflow-discovery');
+    const { registerRepository } = await import('@archon/core');
+    const conversationDb = await import('@archon/core/db/conversations');
+    const codebaseDb = await import('@archon/core/db/codebases');
+    const gitModule = await import('@archon/git');
+
+    (discoverWorkflowsWithConfig as ReturnType<typeof mock>).mockResolvedValueOnce({
+      workflows: [makeTestWorkflowWithSource({ name: 'assist', description: 'Help' })],
+      errors: [],
+    });
+    (conversationDb.getOrCreateConversation as ReturnType<typeof mock>).mockResolvedValueOnce({
+      id: 'conv-123',
+    });
+    (codebaseDb.findCodebaseByDefaultCwd as ReturnType<typeof mock>).mockResolvedValueOnce(null);
+    (gitModule.findRepoRoot as ReturnType<typeof mock>).mockResolvedValueOnce('/test/path');
+    (registerRepository as ReturnType<typeof mock>).mockRejectedValueOnce(
+      new Error(
+        'Source symlink at /home/test/.archon/workspaces/acme/widget/source already points to ' +
+          '/home/test/.archon/workspaces/widget, expected /test/path'
+      )
+    );
+
+    const error = await workflowRunCommand('/test/path', 'assist', 'hello', {}).catch(
+      err => err as Error
+    );
+
+    expect(error).toBeInstanceOf(Error);
+    expect(error.message).toContain('Cannot create worktree: repository registration failed.');
+    expect(error.message).toContain(
+      'Remove the stale workspace entry at /home/test/.archon/workspaces/acme/widget and retry'
+    );
+    expect(error.message).not.toContain('not in a git repository');
+  });
+
+  it('surfaces auto-registration failures on --resume instead of claiming the repo is invalid', async () => {
+    const { discoverWorkflowsWithConfig } = await import('@archon/workflows/workflow-discovery');
+    const { registerRepository } = await import('@archon/core');
+    const conversationDb = await import('@archon/core/db/conversations');
+    const codebaseDb = await import('@archon/core/db/codebases');
+    const gitModule = await import('@archon/git');
+
+    (discoverWorkflowsWithConfig as ReturnType<typeof mock>).mockResolvedValueOnce({
+      workflows: [makeTestWorkflowWithSource({ name: 'assist', description: 'Help' })],
+      errors: [],
+    });
+    (conversationDb.getOrCreateConversation as ReturnType<typeof mock>).mockResolvedValueOnce({
+      id: 'conv-123',
+    });
+    (codebaseDb.findCodebaseByDefaultCwd as ReturnType<typeof mock>).mockResolvedValueOnce(null);
+    (gitModule.findRepoRoot as ReturnType<typeof mock>).mockResolvedValueOnce('/test/path');
+    (registerRepository as ReturnType<typeof mock>).mockRejectedValueOnce(
+      new Error(
+        'Source symlink at /home/test/.archon/workspaces/acme/widget/source already points to ' +
+          '/home/test/.archon/workspaces/widget, expected /test/path'
+      )
+    );
+
+    const error = await workflowRunCommand('/test/path', 'assist', 'hello', {
+      resume: true,
+    }).catch(err => err as Error);
+
+    expect(error).toBeInstanceOf(Error);
+    expect(error.message).toContain('Cannot resume: repository registration failed.');
+    expect(error.message).toContain(
+      'Remove the stale workspace entry at /home/test/.archon/workspaces/acme/widget and retry'
+    );
+    expect(error.message).not.toContain('Not in a git repository');
+  });
+
+  it('falls back to generic workspace hint when registration error has an unrecognized shape', async () => {
+    const { discoverWorkflowsWithConfig } = await import('@archon/workflows/workflow-discovery');
+    const { registerRepository } = await import('@archon/core');
+    const conversationDb = await import('@archon/core/db/conversations');
+    const codebaseDb = await import('@archon/core/db/codebases');
+    const gitModule = await import('@archon/git');
+
+    (discoverWorkflowsWithConfig as ReturnType<typeof mock>).mockResolvedValueOnce({
+      workflows: [makeTestWorkflowWithSource({ name: 'assist', description: 'Help' })],
+      errors: [],
+    });
+    (conversationDb.getOrCreateConversation as ReturnType<typeof mock>).mockResolvedValueOnce({
+      id: 'conv-123',
+    });
+    (codebaseDb.findCodebaseByDefaultCwd as ReturnType<typeof mock>).mockResolvedValueOnce(null);
+    (gitModule.findRepoRoot as ReturnType<typeof mock>).mockResolvedValueOnce('/test/path');
+    (registerRepository as ReturnType<typeof mock>).mockRejectedValueOnce(
+      new Error("EACCES: permission denied, mkdir '/home/test/.archon/workspaces/acme'")
+    );
+
+    const error = await workflowRunCommand('/test/path', 'assist', 'hello', {}).catch(
+      err => err as Error
+    );
+
+    expect(error).toBeInstanceOf(Error);
+    expect(error.message).toContain('Cannot create worktree: repository registration failed.');
+    expect(error.message).toContain('EACCES: permission denied');
+    // Path-separator-agnostic check: on Windows path.join normalizes to `\`,
+    // on POSIX to `/`. Assert the hint prefix + the final segment separately.
+    expect(error.message).toContain('Check your Archon workspace registration under');
+    expect(error.message).toMatch(/workspaces\b/);
+    expect(error.message).not.toContain('Remove the stale workspace entry');
+  });
+
   // -------------------------------------------------------------------------
   // Workflow-level `worktree.enabled` policy
   // -------------------------------------------------------------------------
@@ -2410,3 +2518,51 @@ describe('workflowRunCommand — progress rendering', () => {
     expect(stderrSpy).toHaveBeenCalledWith('[slow] Completed (1m30s)\n');
   });
 });
+
+// ---------------------------------------------------------------------------
+// extractStaleWorkspaceEntry — parser edge cases
+// ---------------------------------------------------------------------------
+
+describe('extractStaleWorkspaceEntry', () => {
+  it('extracts the workspace dir from a POSIX source-symlink error', async () => {
+    const { extractStaleWorkspaceEntry } = await import('./workflow');
+    expect(
+      extractStaleWorkspaceEntry(
+        'Source symlink at /home/user/.archon/workspaces/acme/widget/source already points to /other, expected /here'
+      )
+    ).toBe('/home/user/.archon/workspaces/acme/widget');
+  });
+
+  it('extracts the workspace dir from a Windows source-symlink error (backslash sep)', async () => {
+    const { extractStaleWorkspaceEntry } = await import('./workflow');
+    expect(
+      extractStaleWorkspaceEntry(
+        'Source symlink at C:\\Users\\me\\.archon\\workspaces\\acme\\widget\\source already points to D:\\x, expected D:\\y'
+      )
+    ).toBe('C:\\Users\\me\\.archon\\workspaces\\acme\\widget');
+  });
+
+  it('returns null when the prefix does not match (unrelated error)', async () => {
+    const { extractStaleWorkspaceEntry } = await import('./workflow');
+    expect(extractStaleWorkspaceEntry('ENOENT: no such file or directory')).toBeNull();
+  });
+
+  it('returns null when the prefix matches but the delimiter is missing', async () => {
+    const { extractStaleWorkspaceEntry } = await import('./workflow');
+    expect(
+      extractStaleWorkspaceEntry('Source symlink at /some/path (truncated message)')
+    ).toBeNull();
+  });
+
+  it('returns null when the source path has no path separator at all', async () => {
+    const { extractStaleWorkspaceEntry } = await import('./workflow');
+    expect(
+      extractStaleWorkspaceEntry('Source symlink at bareword already points to /x, expected /y')
+    ).toBeNull();
+  });
+
+  it('returns null on an empty input', async () => {
+    const { extractStaleWorkspaceEntry } = await import('./workflow');
+    expect(extractStaleWorkspaceEntry('')).toBeNull();
+  });
+});
@@ -10,7 +10,8 @@ import {
 } from '@archon/core';
 import { WORKFLOW_EVENT_TYPES, type WorkflowEventType } from '@archon/workflows/store';
 import { configureIsolation, getIsolationProvider } from '@archon/isolation';
-import { createLogger } from '@archon/paths';
+import { createLogger, getArchonHome } from '@archon/paths';
+import { join } from 'node:path';
 import { createWorkflowDeps } from '@archon/core/workflows/store-adapter';
 import { discoverWorkflowsWithConfig } from '@archon/workflows/workflow-discovery';
 import { resolveWorkflowName } from '@archon/workflows/router';
@@ -77,6 +78,57 @@ function generateConversationId(): string {
   return `cli-${String(timestamp)}-${random}`;
 }
 
+/**
+ * Parses the "Source symlink at X already points to Y, expected Z" error
+ * thrown by `createProjectSourceSymlink` in @archon/paths. Cross-package
+ * string contract — if that throw site changes wording, this parser silently
+ * stops matching. Returns the workspace dir (parent of the `source` link) so
+ * the caller can emit an exact cleanup path, or null if unrecognized.
+ */
+export function extractStaleWorkspaceEntry(message: string): string | null {
+  const prefix = 'Source symlink at ';
+  const delimiter = ' already points to ';
+  if (!message.startsWith(prefix)) return null;
+
+  const remainder = message.slice(prefix.length);
+  const delimiterIndex = remainder.indexOf(delimiter);
+  if (delimiterIndex === -1) return null;
+
+  const sourcePath = remainder.slice(0, delimiterIndex).trim();
+  const lastSeparator = Math.max(sourcePath.lastIndexOf('/'), sourcePath.lastIndexOf('\\'));
+  return lastSeparator === -1 ? null : sourcePath.slice(0, lastSeparator);
+}
+
+/**
+ * Wraps a codebase auto-registration failure for either the worktree-create or
+ * resume path. Preserves the original error message and delegates hint detail
+ * to `extractStaleWorkspaceEntry`; falls back to a workspace-root pointer when
+ * the error shape is unrecognized.
+ */
+function buildRegistrationFailureError(action: string, error: Error): Error {
+  const staleWorkspaceEntry = extractStaleWorkspaceEntry(error.message);
+  let hint: string;
+  if (staleWorkspaceEntry) {
+    hint = `Hint: Remove the stale workspace entry at ${staleWorkspaceEntry} and retry, or use --no-worktree to skip isolation.`;
+  } else {
+    // Guard against a throwing getArchonHome() (misconfigured env vars, etc.):
+    // the registration error we're wrapping is the load-bearing one — we'd
+    // rather lose the exact path in the hint than replace it with a secondary
+    // home-resolution error that masks the root cause.
+    try {
+      const workspacesPath = join(getArchonHome(), 'workspaces');
+      hint = `Hint: Check your Archon workspace registration under ${workspacesPath} and retry, or use --no-worktree to skip isolation.`;
+    } catch {
+      hint =
+        'Hint: Check your Archon workspace registration and retry, or use --no-worktree to skip isolation.';
+    }
+  }
+
+  return new Error(
+    `Cannot ${action}: repository registration failed.\nError: ${error.message}\n${hint}`
+  );
+}
+
 /** Render a workflow event to stderr as a progress line. Called only when --quiet is not set. */
 function renderWorkflowEvent(event: WorkflowEmitterEvent, verbose: boolean): void {
   switch (event.type) {
@@ -316,6 +368,7 @@ export async function workflowRunCommand(
   // Try to find a codebase for this directory
   let codebase = null;
   let codebaseLookupError: Error | null = null;
+  let codebaseRegistrationError: Error | null = null;
   try {
     codebase = await codebaseDb.findCodebaseByDefaultCwd(cwd);
   } catch (error) {
@@ -361,6 +414,7 @@ export async function workflowRunCommand(
         }
       } catch (error) {
         const err = error as Error;
+        codebaseRegistrationError = err;
         getLog().warn(
           { err, errorType: err.constructor.name, repoRoot },
           'cli.codebase_auto_registration_failed'
@@ -385,6 +439,9 @@ export async function workflowRunCommand(
             'Hint: Check your database connection before using --resume.'
         );
       }
+      if (codebaseRegistrationError) {
+        throw buildRegistrationFailureError('resume', codebaseRegistrationError);
+      }
       throw new Error(
         'Cannot resume: Not in a git repository.\n' +
           'Either run from a git repo or use /clone first.'
@@ -544,6 +601,9 @@ export async function workflowRunCommand(
           'Hint: Check your database connection, or use --no-worktree to skip isolation.'
       );
     }
+    if (codebaseRegistrationError) {
+      throw buildRegistrationFailureError('create worktree', codebaseRegistrationError);
+    }
     throw new Error(
       'Cannot create worktree: not in a git repository.\n' +
         'Run from within a git repo, or use --no-worktree to skip isolation.'
 
@@ -482,17 +482,19 @@ The CLI is standalone, but if you also want to interact via Telegram, Slack, Dis
 
 ## Troubleshooting
 
-### "Cannot create worktree: not in a git repository" (but the repo exists)
+### "Cannot create worktree: repository registration failed" (stale workspace symlink)
 
-The real cause is usually a stale symlink from a previous Archon run with a different path. Look for this in the error output:
+This happens when `~/.archon/workspaces/<owner>/<repo>/source` is a symlink pointing at a previous checkout (common after moving or renaming the repo). The error message includes the exact cleanup path to follow:
 
 ```
-Source symlink at ~/.archon/workspaces/.../source already points to <old-path>, expected <new-path>
+Cannot create worktree: repository registration failed.
+Error: Source symlink at ~/.archon/workspaces/<owner>/<repo>/source already points to <old-path>, expected <new-path>
+Hint: Remove the stale workspace entry at ~/.archon/workspaces/<owner>/<repo> and retry, or use --no-worktree to skip isolation.
 ```
 
-Fix it by manually deleting the stale workspace folder at `~/.archon/workspaces/<github-user>/<repo-name>` and retrying the command.
+Follow the hint — delete the stale workspace folder and re-run, or pass `--no-worktree` to skip isolation for one run.
 
-> In the future, `archon isolation cleanup` will handle this automatically.
+> On Archon versions before this fix, the same root cause surfaced as the misleading "Cannot create worktree: not in a git repository" (even though the repo was valid). If you see that string, upgrade and you'll get the actionable message above.
 
 ---