diff --git a/ADOPTING.md b/ADOPTING.md
index 2d232d4..68f5f91 100644
--- a/ADOPTING.md
+++ b/ADOPTING.md
@@ -26,7 +26,7 @@ What you do **not** copy: HANDBOOK.md, the `methodology` domain, `examples/`, `t
 curl -fsSL https://raw.githubusercontent.com/emafriedrich/knowledge-driven-engineering/main/install.sh | bash -s -- <your-first-domain>
 ```
 
-`install.sh` performs the manual steps below, is idempotent, and never overwrites an existing file (it skips and tells you). It detects your package manager (npm, pnpm — workspaces included, yarn, bun) for the `yaml` dependency, and a dependency failure warns instead of aborting the install. Run it from the root of your repository; pass your first domain name as the argument. The argument only seeds a fresh install: on a repository that already has `knowledge/index.yaml` the installer creates no domain and points you to `npm run knowledge -- domain add <name>`. Installing, upgrading (`--upgrade`) and adding a domain are three separate actions. Offline installs work from a local clone: `KDE_SOURCE=/path/to/clone bash install.sh <domain>`. To pin a release instead of tracking `main`, set `KDE_REF=v0.1.0`.
+`install.sh` performs the manual steps below, is idempotent, and never overwrites an existing file (it skips and tells you). It detects your package manager (npm, pnpm — workspaces included, yarn, bun) for the `yaml` dependency, and a dependency failure warns instead of aborting the install. Run it from the root of your repository; pass your first domain name as the argument. It refuses to run in a subdirectory of a repository that already runs KDE — a second catalog nothing reads — and names the directory to run it from. The argument only seeds a fresh install: on a repository that already has `knowledge/index.yaml` the installer creates no domain and points you to `npm run knowledge -- domain add <name>`. Installing, upgrading (`--upgrade`) and adding a domain are three separate actions. Offline installs work from a local clone: `KDE_SOURCE=/path/to/clone bash install.sh <domain>`. To pin a release instead of tracking `main`, set `KDE_REF=v0.1.0`.
 
 ## Upgrading
 
diff --git a/install.sh b/install.sh
index 94c731f..c169730 100755
--- a/install.sh
+++ b/install.sh
@@ -39,6 +39,23 @@ say()  { printf '%s\n' "$*"; }
 add()  { say "  add   $1"; }
 skip() { say "  skip  $1 (already exists)"; }
 
+# A repository runs one knowledge catalog. Installing below a directory of the
+# same git repository that already has one creates a second, empty KDE that
+# nothing reads — refuse and name the right directory instead.
+TOPLEVEL="$(git rev-parse --show-toplevel 2>/dev/null || true)"
+if [ -n "$TOPLEVEL" ]; then
+  HERE="$(pwd -P)"
+  TOPLEVEL="$(cd "$TOPLEVEL" && pwd -P)"
+  dir="$HERE"
+  while [ "$dir" != "$TOPLEVEL" ] && [ "$dir" != "/" ]; do
+    dir="$(dirname "$dir")"
+    if [ -f "$dir/knowledge/index.yaml" ] && [ -f "$dir/tools/knowledge-check.mts" ]; then
+      say "install.sh: ${dir} already runs Knowledge-Driven Engineering; run the installer from there, not from ${HERE}." >&2
+      exit 1
+    fi
+  done
+fi
+
 # Version of the framework-owned files a repository runs, read from the
 # kde-version marker the installer stamps on line 1 of every copy.
 installed_version() {
@@ -403,7 +420,10 @@ fi
 say ""
 say "Done. Next steps:"
 say "  1. npm run knowledge:check"
-say "  2. Seed current truth with one decision your team already made:"
+say "  2. Existing codebase? Recover the behavior that lives only in code, one domain at a time:"
+say "       npm run knowledge -- backfill ${DOMAIN:-<domain>}"
+say "     then ask your coding agent to \"backfill the ${DOMAIN:-<domain>} domain\" — it follows tools/backfill-protocol.md."
+say "     Starting fresh? Seed current truth with one decision your team already made:"
 say "       npm run knowledge -- new decision ${DOMAIN:-<domain>} \"<title>\" --author <you>"
 say "       npm run knowledge -- promote <ID> --by <you>"
 say "  3. Enable branch protection with code-owner review so knowledge promotion needs a human."
diff --git a/package.json b/package.json
index b581ac2..dbe7af6 100644
--- a/package.json
+++ b/package.json
@@ -1,6 +1,6 @@
 {
   "name": "knowledge-driven-engineering",
-  "version": "0.7.1",
+  "version": "0.7.2",
   "private": true,
   "type": "module",
   "scripts": {
diff --git a/tests/install.test.ts b/tests/install.test.ts
index bfa6631..0c21f59 100644
--- a/tests/install.test.ts
+++ b/tests/install.test.ts
@@ -1,6 +1,6 @@
 import assert from 'node:assert/strict';
 import { execFileSync } from 'node:child_process';
-import { appendFileSync, existsSync, mkdtempSync, readFileSync, rmSync, writeFileSync } from 'node:fs';
+import { appendFileSync, existsSync, mkdirSync, mkdtempSync, readFileSync, rmSync, writeFileSync } from 'node:fs';
 import { tmpdir } from 'node:os';
 import { join, resolve } from 'node:path';
 import test from 'node:test';
@@ -83,6 +83,24 @@ test('installer stamps framework-owned files with the package.json version and r
   }
 });
 
+test('installer refuses a subdirectory of a repository that already runs KDE, and suggests backfill as a next step', () => {
+  const root = mkdtempSync(join(tmpdir(), 'kde-install-test-'));
+  try {
+    execFileSync('git', ['init', '-q'], { cwd: root });
+    const fresh = install(root, 'shop');
+    assert.match(fresh, /Existing codebase\? Recover the behavior that lives only in code[\s\S]*npm run knowledge -- backfill shop[\s\S]*"backfill the shop domain" — it follows tools\/backfill-protocol\.md/);
+    assert.match(fresh, /Starting fresh\? Seed current truth/);
+
+    const nested = join(root, 'apps', 'api');
+    mkdirSync(nested, { recursive: true });
+    assert.throws(() => install(nested, '--upgrade'), /already runs Knowledge-Driven Engineering; run the installer from there, not from .*apps\/api/);
+    assert.equal(existsSync(join(nested, 'knowledge')), false, 'nothing is written in the subdirectory');
+    assert.equal(existsSync(join(nested, 'tools')), false);
+  } finally {
+    rmSync(root, { recursive: true, force: true });
+  }
+});
+
 test('installer rejects unknown options', () => {
   const root = mkdtempSync(join(tmpdir(), 'kde-install-test-'));
   try {
diff --git a/tests/knowledge.test.ts b/tests/knowledge.test.ts
index c1a15b4..42bc853 100644
--- a/tests/knowledge.test.ts
+++ b/tests/knowledge.test.ts
@@ -334,6 +334,12 @@ test('prompt: new scaffolds from the template and promote sets current — promp
   });
 });
 
+test('a command run where the catalog has no domains says the directory may be the wrong one', () => {
+  withFixture({ 'knowledge/index.yaml': 'domains: {}\n' }, (root) => {
+    assert.throws(() => commandBackfill(root, 'orders'), /has no domains at all — if this repository runs KDE from another directory, run the command there/);
+  });
+});
+
 test('cli: usage errors are CommandErrors, and flags with several values are collected', () => {
   withFixture({}, (root) => {
     assert.throws(() => run(root, ['promote']), /usage:/);
diff --git a/tools/knowledge.mts b/tools/knowledge.mts
index 85a2b40..aa4f94f 100644
--- a/tools/knowledge.mts
+++ b/tools/knowledge.mts
@@ -124,10 +124,14 @@ function slugify(text: string): string {
 // --- Repository lookups -----------------------------------------------------
 
 function findDomain(root: string, name: string): { catalog: Catalog; domain: CatalogDomain } {
-  for (const catalog of loadCatalogs(root)) {
+  const catalogs = loadCatalogs(root);
+  for (const catalog of catalogs) {
     const domain = catalog.domains.get(name);
     if (domain) return { catalog, domain };
   }
+  if (catalogs.every((catalog) => catalog.domains.size === 0)) {
+    throw new CommandError(`domain ${name} is not in any catalog, and the catalog in ${root} has no domains at all — if this repository runs KDE from another directory, run the command there; otherwise create it: npm run knowledge -- domain add ${name} --description "<one line>"`);
+  }
   throw new CommandError(`domain ${name} is not in any catalog — create it: npm run knowledge -- domain add ${name} --description "<one line>"`);
 }