diff --git a/doc/DEVELOPING.md b/doc/DEVELOPING.md
index 7fdd364f4a..5d37d441c8 100644
--- a/doc/DEVELOPING.md
+++ b/doc/DEVELOPING.md
@@ -824,6 +824,7 @@ The default `worktree init` still seeds eagerly. A lean worktree (created withou
 - `pnpm paperclipai worktree ensure-seeded` performs the deferred seed **exactly once**. It is lock-guarded and idempotent: only a complete `verified` manifest short-circuits it, so it is safe to call repeatedly and from concurrent processes. Managed workspaces derive the source from the control-plane-provided base project workspace when it carries its own `.paperclip/config.json`, and otherwise from the control plane's own registered instance config; either way the workspace's manifest never selects it. Manual worktrees must pass `--from-config`.
 - `paperclipai run` calls `ensureWorktreeSeeded` automatically before doctor/boot. Managed runs transparently seed a lean worktree from their registered base workspace; an unmanaged lean worktree must first run `worktree ensure-seeded --from-config <source-config>`.
 - Managed Paperclip git worktrees default to the repository's `scripts/provision-worktree.sh` when the strategy omits `provisionCommand`, so the isolated config and pending manifest cannot be silently skipped. Runtime startup also runs `scripts/provision-worktree-runtime.sh` automatically when no explicit runtime provision command is configured and the manifest is not verified. Explicitly configured provision commands still take precedence.
+- If the built-in provisioner reports an unavailable seed source config, decide whether the task needs a seeded development instance or only an isolated checkout. A seeded instance needs a canonical config from the registered base workspace or control-plane instance; environment-only server configuration does not provide that file. For a checkout-only worktree, explicitly set the `git_worktree` strategy's `provisionCommand` to `"true"`. This skips setup and does not establish runtime or seed readiness. Repair rejected symlinks or non-regular source files instead of treating those validation failures as a missing prerequisite.
 - The built-in deferred seed is recorded as its own terminal `workspace_seed` operation. A zero exit code is not enough for success: the operation succeeds only when `.paperclip/seed-manifest.json` contains complete verified evidence; failed, missing, or malformed manifests produce a failed operation with the seed phase in metadata.
 - Worktrees created before lazy seeding shipped may have neither marker. Paperclip adopts them only after their configured database proves a compatible migration journal and the core Paperclip schema; otherwise managed startup creates a pending manifest and performs the normal verified seed. Manual markerless worktrees must provide `--from-config` so the source remains explicit.
 
diff --git a/scripts/__tests__/provision-worktree-self-heal.test.mjs b/scripts/__tests__/provision-worktree-self-heal.test.mjs
index 943a15f48b..bff638cdc4 100644
--- a/scripts/__tests__/provision-worktree-self-heal.test.mjs
+++ b/scripts/__tests__/provision-worktree-self-heal.test.mjs
@@ -102,11 +102,12 @@ process.exit(0);
   return baseCwd;
 }
 
-function runProvision(baseCwd, { pathPrefix, setupWorktree, existingWorktree } = {}) {
+function runProvision(baseCwd, { pathPrefix, setupWorktree, setupInstance, existingWorktree } = {}) {
   const worktreeCwd = existingWorktree ?? makeTempDir("paperclip-provision-worktree-");
   setupWorktree?.(worktreeCwd);
   const worktreesHome = makeTempDir("paperclip-provision-home-");
   const paperclipHome = makeInstanceHome();
+  setupInstance?.(paperclipHome);
   const result = spawnSync("bash", [script], {
     cwd: worktreeCwd,
     encoding: "utf8",
@@ -182,15 +183,52 @@ test("uses the base CLI when its import graph boots", () => {
   );
 });
 
+test("explains unavailable instance source config without creating target state", () => {
+  const baseCwd = makeBaseWorkspace({ helpExit: 0, initExit: 0 });
+  const { result, worktreeCwd } = runProvision(baseCwd, {
+    setupInstance: (home) => fs.rmSync(path.join(home, "instances", "default", "config.json")),
+  });
+
+  assert.notEqual(result.status, 0);
+  assert.match(result.stderr, /config is unavailable \(control-plane instance\)/);
+  assert.match(result.stderr, /For a seeded development instance, configure a canonical config/);
+  assert.match(result.stderr, /Only for a checkout-only worktree/);
+  assert.match(result.stderr, /workspaceStrategy\.provisionCommand to "true"/);
+  assert.match(result.stderr, /does not prepare a development runtime/);
+  assert.equal(fs.existsSync(path.join(worktreeCwd, ".paperclip")), false);
+  assert.deepEqual(readCliInvocations(baseCwd), []);
+});
+
 test("rejects a dangling base workspace config symlink instead of falling back", () => {
   const baseCwd = makeBaseWorkspace({ helpExit: 0, initExit: 0 });
   fs.mkdirSync(path.join(baseCwd, ".paperclip"), { recursive: true });
   fs.symlinkSync(path.join(baseCwd, "absent.json"), path.join(baseCwd, ".paperclip", "config.json"));
 
-  const { result } = runProvision(baseCwd);
+  const { result, worktreeCwd } = runProvision(baseCwd);
 
   assert.notEqual(result.status, 0);
-  assert.match(result.stderr, /is missing or is not a canonical file/);
+  assert.match(result.stderr, /is not a canonical file \(base project workspace\)/);
+  assert.doesNotMatch(result.stderr, /checkout-only|provisionCommand/);
+  assert.equal(fs.existsSync(path.join(worktreeCwd, ".paperclip")), false);
+  assert.deepEqual(readCliInvocations(baseCwd), []);
+});
+
+test("rejects a non-regular instance config without suggesting a setup bypass", () => {
+  const baseCwd = makeBaseWorkspace({ helpExit: 0, initExit: 0 });
+  const { result, worktreeCwd } = runProvision(baseCwd, {
+    setupInstance: (home) => {
+      const configPath = path.join(home, "instances", "default", "config.json");
+      fs.rmSync(configPath);
+      fs.mkdirSync(configPath);
+    },
+  });
+
+  assert.notEqual(result.status, 0);
+  assert.match(result.stderr, /is not a canonical file \(control-plane instance\)/);
+  assert.match(result.stderr, /Repair the registered source path/);
+  assert.doesNotMatch(result.stderr, /checkout-only|provisionCommand/);
+  assert.equal(fs.existsSync(path.join(worktreeCwd, ".paperclip")), false);
+  assert.deepEqual(readCliInvocations(baseCwd), []);
 });
 
 test("rejects a dangling base workspace .paperclip symlink instead of falling back", () => {
diff --git a/scripts/provision-worktree.sh b/scripts/provision-worktree.sh
index af7c61b1a8..2418fa3bb0 100644
--- a/scripts/provision-worktree.sh
+++ b/scripts/provision-worktree.sh
@@ -48,14 +48,23 @@ if [[ -L "$canonical_base_cwd/.paperclip" && ! -d "$canonical_base_cwd/.papercli
   exit 1
 fi
 source_config_path="$canonical_base_cwd/.paperclip/config.json"
+source_config_origin="base project workspace"
 if [[ ! -e "$source_config_path" && ! -L "$source_config_path" ]]; then
   # A base workspace that is a plain checkout carries no instance config of its own.
   # Fall back to the control plane's own registered instance config, which is process
   # state this workspace cannot rewrite.
   source_config_path="${PAPERCLIP_CONFIG:-$paperclip_home/instances/$paperclip_instance_id/config.json}"
+  source_config_origin="control-plane instance"
 fi
 if [[ ! -f "$source_config_path" || -L "$source_config_path" ]]; then
-  echo "Registered Paperclip seed source config is missing or is not a canonical file: $source_config_path" >&2
+  if [[ ! -e "$source_config_path" && ! -L "$source_config_path" ]]; then
+    echo "Registered Paperclip seed source config is unavailable ($source_config_origin): $source_config_path" >&2
+    echo "For a seeded development instance, configure a canonical config for that registered source before retrying." >&2
+    echo 'Only for a checkout-only worktree, explicitly set workspaceStrategy.provisionCommand to "true". This skips setup; it does not prepare a development runtime.' >&2
+  else
+    echo "Registered Paperclip seed source config is not a canonical file ($source_config_origin): $source_config_path" >&2
+    echo "Repair the registered source path; symlinks and non-regular files are not accepted." >&2
+  fi
   exit 1
 fi
 canonical_source_dir="$(cd "$(dirname "$source_config_path")" && pwd -P)"