diff --git a/CHANGELOG.md b/CHANGELOG.md
index 3ff759f..ecaf935 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -7,6 +7,22 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## [Unreleased]
 
+## [1.0.0-beta.3]
+
+### Added
+
+- `sourceant stop` shuts down the local stack without removing its data.
+- Core and agent releases can be selected independently during setup.
+
+### Fixed
+
+- Installation finds a release when only prereleases are available.
+
+### Compatibility
+
+- `sourceant stop` requires agent `1.0.0-beta.3` or later with shutdown support.
+- Core compatibility is determined by the installed agent.
+
 ## [1.0.0-beta.2] - 2026-08-30
 
 First release, versioned alongside the core it reads.
diff --git a/README.md b/README.md
index 1d6307d..6ecfaf9 100644
--- a/README.md
+++ b/README.md
@@ -42,7 +42,23 @@ sourceant setup
 
 `setup` puts the agent and a core on this machine and writes down which one, so the agent knows what to start.
 
-Two ways to have it. `--runtime docker` pulls the published image, and is what works today. `--runtime python` builds a virtual environment and pip installs the core, for when the core is published as a package; until then it says so rather than recording something that will not start.
+`--runtime docker` pulls the published image. `--runtime python` builds a virtual environment and installs the core's published wheel.
+
+The core and agent versions are independent of the CLI version. By default, Docker uses the `latest` image, Python uses the latest core release, and the agent uses its latest release. Release lookup prefers a stable release and falls back to the newest published prerelease when no stable release exists. The CLI installer uses the same policy.
+
+Pin releases independently:
+
+```bash
+sourceant setup --core-version 1.0.0-beta.2 --agent-version 1.0.0-beta.2
+```
+
+`--core-version` selects a `v`-prefixed image tag for Docker or a release wheel for Python. Use `--image` for a custom container image or `--from` for a Python package specifier or checkout. Neither can be combined with `--core-version`.
+
+To pin the CLI installer itself:
+
+```bash
+curl -fsSL https://raw.githubusercontent.com/sourceant/cli/main/scripts/install.sh | SOURCEANT_VERSION=1.0.0-beta.2 sh
+```
 
 Both put the index in the same place, `$XDG_DATA_HOME/sourceant`, so it does not matter which one indexed it. The container runs as whoever installed, so what it writes there belongs to them.
 
@@ -78,3 +94,13 @@ make build
 ## Licence
 
 MIT.
+
+## Versioning
+
+The CLI is versioned independently of the core, agent, and design package. A CLI release does not require matching releases of the components it installs. Use `--core-version` and `--agent-version` to select them separately, or `--image` and `--from` to choose the core directly.
+
+CLI `1.0.0-beta.3` requires agent `1.0.0-beta.3` for `sourceant stop`. The agent defines core compatibility. For a reproducible setup, select both explicitly:
+
+```bash
+sourceant setup --agent-version 1.0.0-beta.3 --core-version 1.0.0-beta.2
+```
diff --git a/VERSION b/VERSION
index 7e0b231..b0a2ffd 100644
--- a/VERSION
+++ b/VERSION
@@ -1 +1 @@
-1.0.0-beta.2
+1.0.0-beta.3
diff --git a/internal/command/setup.go b/internal/command/setup.go
index e6b31ca..af09429 100644
--- a/internal/command/setup.go
+++ b/internal/command/setup.go
@@ -10,11 +10,13 @@ import (
 
 func setupCommand() *cobra.Command {
 	var (
-		runtime string
-		image   string
-		from    string
-		noPull  bool
-		noAgent bool
+		coreVersion  string
+		agentVersion string
+		runtime      string
+		image        string
+		from         string
+		noPull       bool
+		noAgent      bool
 	)
 	command := &cobra.Command{
 		Use:   "setup",
@@ -35,7 +37,7 @@ func setupCommand() *cobra.Command {
 				Image:   image,
 				From:    from,
 				Pull:    !noPull,
-				Version: Version,
+				Version: coreVersion,
 				Out:     cmd.OutOrStdout(),
 			}, install.Run)
 			if err != nil {
@@ -56,7 +58,7 @@ func setupCommand() *cobra.Command {
 			_, _ = fmt.Fprintf(out, "Written to %s\n\n", path)
 
 			if !noAgent {
-				agentPath, err := install.InstallAgent(Version, install.Get, out)
+				agentPath, err := install.InstallAgent(agentVersion, install.Get, out)
 				if err != nil {
 					return fmt.Errorf("the core is installed, but the agent is not: %w", err)
 				}
@@ -67,10 +69,14 @@ func setupCommand() *cobra.Command {
 			return nil
 		},
 	}
+	command.Flags().StringVar(&coreVersion, "core-version", "latest", "Core release to install, independently of the CLI")
+	command.Flags().StringVar(&agentVersion, "agent-version", "latest", "Agent release to install, independently of the CLI")
 	command.Flags().StringVar(&runtime, "runtime", string(install.Docker), "docker or python. Chosen for you when not named")
-	command.Flags().StringVar(&image, "image", install.DefaultImage, "The container to use, for the docker runtime")
-	command.Flags().StringVar(&from, "from", "", "What pip installs, for the python runtime. Defaults to the wheel this version published")
+	command.Flags().StringVar(&image, "image", "", "The container to use, for the docker runtime")
+	command.Flags().StringVar(&from, "from", "", "What pip installs, for the python runtime. Defaults to the selected core release wheel")
 	command.Flags().BoolVar(&noPull, "no-pull", false, "Use an image already on this machine")
 	command.Flags().BoolVar(&noAgent, "no-agent", false, "Leave the agent alone, install only the core")
+	command.MarkFlagsMutuallyExclusive("core-version", "image")
+	command.MarkFlagsMutuallyExclusive("core-version", "from")
 	return command
 }
diff --git a/internal/command/setup_test.go b/internal/command/setup_test.go
new file mode 100644
index 0000000..130837a
--- /dev/null
+++ b/internal/command/setup_test.go
@@ -0,0 +1,183 @@
+package command
+
+import (
+	"bytes"
+	"net/http"
+	"net/http/httptest"
+	"os"
+	"os/exec"
+	"path/filepath"
+	"strings"
+	"testing"
+)
+
+func TestSetupVersionsAreIndependent(t *testing.T) {
+	previous := Version
+	Version = "unrelated-cli-version"
+	t.Cleanup(func() { Version = previous })
+	for _, tc := range []struct {
+		name string
+		args []string
+		want string
+	}{
+		{"docker default", []string{"--runtime", "docker"}, "ghcr.io/sourceant/sourceant:latest"},
+		{"docker pinned", []string{"--runtime", "docker", "--core-version", "1.0.0-beta.2"}, "ghcr.io/sourceant/sourceant:v1.0.0-beta.2"},
+		{"docker custom", []string{"--runtime", "docker", "--image", "custom:local"}, "custom:local"},
+		{"python default", []string{"--runtime", "python"}, "v1.0.0-beta.2/sourceant-1.0.0b2-py3-none-any.whl"},
+		{"python pinned", []string{"--runtime", "python", "--core-version", "v1.0.0-beta.2"}, "v1.0.0-beta.2/sourceant-1.0.0b2-py3-none-any.whl"},
+		{"python custom", []string{"--runtime", "python", "--from", "./local-core"}, "./local-core"},
+	} {
+		t.Run(tc.name, func(t *testing.T) {
+			home := t.TempDir()
+			t.Setenv("SOURCEANT_INSTALL_HOME", home)
+			t.Setenv("SOURCEANT_HOME", filepath.Join(home, "data"))
+			t.Setenv("CALLS", filepath.Join(home, "calls"))
+			bin := filepath.Join(home, "bin")
+			if err := os.MkdirAll(bin, 0755); err != nil {
+				t.Fatal(err)
+			}
+			for name, body := range map[string]string{
+				"docker":  "#!/bin/sh\nprintf '%s\\n' \"$*\" >> \"$CALLS\"\n",
+				"python3": "#!/bin/sh\nexit 0\n",
+			} {
+				if err := os.WriteFile(filepath.Join(bin, name), []byte(body), 0755); err != nil {
+					t.Fatal(err)
+				}
+			}
+			runtimeBin := filepath.Join(home, "runtime", "bin")
+			if err := os.MkdirAll(runtimeBin, 0755); err != nil {
+				t.Fatal(err)
+			}
+			for _, name := range []string{"pip", "sourceant"} {
+				if err := os.WriteFile(filepath.Join(runtimeBin, name), []byte("#!/bin/sh\nprintf '%s\\n' \"$*\" >> \"$CALLS\"\n"), 0755); err != nil {
+					t.Fatal(err)
+				}
+			}
+			t.Setenv("PATH", bin+string(os.PathListSeparator)+os.Getenv("PATH"))
+			server := httptest.NewServer(http.HandlerFunc(func(w http.ResponseWriter, r *http.Request) {
+				if r.URL.Path != "/latest" {
+					t.Errorf("unexpected lookup: %s", r.URL)
+					http.NotFound(w, r)
+					return
+				}
+				data, err := os.ReadFile("testdata/releases/core.json")
+				if err != nil {
+					t.Error(err)
+					return
+				}
+				_, _ = w.Write(data)
+			}))
+			defer server.Close()
+			t.Setenv("SOURCEANT_CORE_API_BASE", server.URL)
+			var out, stderr bytes.Buffer
+			if code := Run(append([]string{"setup", "--no-agent"}, tc.args...), &out, &stderr); code != 0 {
+				t.Fatalf("%s", stderr.String())
+			}
+			calls, err := os.ReadFile(filepath.Join(home, "calls"))
+			if err != nil {
+				t.Fatal(err)
+			}
+			if !strings.Contains(string(calls), tc.want) {
+				t.Fatalf("wanted %s in %s", tc.want, calls)
+			}
+		})
+	}
+}
+
+func TestSetupResolvesAgentIndependently(t *testing.T) {
+	previous := Version
+	Version = "unrelated-cli-version"
+	t.Cleanup(func() { Version = previous })
+	for _, pinned := range []bool{false, true} {
+		t.Run(map[bool]string{false: "latest", true: "pinned"}[pinned], func(t *testing.T) {
+			home := t.TempDir()
+			t.Setenv("SOURCEANT_INSTALL_HOME", home)
+			t.Setenv("SOURCEANT_HOME", filepath.Join(home, "data"))
+			if err := os.WriteFile(filepath.Join(home, "docker"), []byte("#!/bin/sh\nexit 0\n"), 0755); err != nil {
+				t.Fatal(err)
+			}
+			t.Setenv("PATH", home+string(os.PathListSeparator)+os.Getenv("PATH"))
+			var paths []string
+			server := httptest.NewServer(http.HandlerFunc(func(w http.ResponseWriter, r *http.Request) {
+				paths = append(paths, r.URL.RequestURI())
+				if r.URL.RawQuery == "per_page=1" {
+					data, err := os.ReadFile("testdata/releases/agent.json")
+					if err != nil {
+						t.Error(err)
+						return
+					}
+					_, _ = w.Write(data)
+					return
+				}
+				http.NotFound(w, r)
+			}))
+			defer server.Close()
+			t.Setenv("SOURCEANT_API_BASE", server.URL)
+			t.Setenv("SOURCEANT_DOWNLOAD_BASE", server.URL)
+			args := []string{"setup", "--runtime", "docker"}
+			if pinned {
+				args = append(args, "--agent-version", "v1.0.0-beta.2")
+			}
+			var out, stderr bytes.Buffer
+			if Run(args, &out, &stderr) == 0 {
+				t.Fatal("download should fail")
+			}
+			if !strings.Contains(stderr.String(), "could not fetch the agent") {
+				t.Fatal(stderr.String())
+			}
+			if !strings.Contains(paths[len(paths)-1], "/v1.0.0-beta.2/sourceant-agent-1.0.0-beta.2-") {
+				t.Fatal(paths)
+			}
+			if pinned && len(paths) != 1 {
+				t.Fatal(paths)
+			}
+			if !pinned && (len(paths) != 3 || paths[0] != "/latest" || paths[1] != "/?per_page=1") {
+				t.Fatal(paths)
+			}
+		})
+	}
+}
+
+func TestInstallerResolvesPrerelease(t *testing.T) {
+	var paths []string
+	server := httptest.NewServer(http.HandlerFunc(func(w http.ResponseWriter, r *http.Request) {
+		paths = append(paths, r.URL.RequestURI())
+		if r.URL.RawQuery == "per_page=1" {
+			data, err := os.ReadFile("testdata/releases/cli.json")
+			if err != nil {
+				t.Error(err)
+				return
+			}
+			_, _ = w.Write(data)
+			return
+		}
+		http.NotFound(w, r)
+	}))
+	defer server.Close()
+	t.Setenv("SOURCEANT_VERSION", "latest")
+	t.Setenv("SOURCEANT_API_BASE", server.URL)
+	t.Setenv("SOURCEANT_DOWNLOAD_BASE", server.URL)
+	cmd := exec.Command("sh", "../../scripts/install.sh")
+	out, err := cmd.CombinedOutput()
+	if err == nil {
+		t.Fatal("download should fail")
+	}
+	if !strings.Contains(string(out), "could not download") {
+		t.Fatal(string(out))
+	}
+	if len(paths) != 3 || paths[0] != "/latest" || paths[1] != "/?per_page=1" || !strings.Contains(paths[2], "/v1.0.0-beta.2/sourceant-1.0.0-beta.2-") {
+		t.Fatal(paths)
+	}
+}
+
+func TestSetupRejectsConflictingCoreSelection(t *testing.T) {
+	for _, flag := range []string{"--image", "--from"} {
+		var out, stderr bytes.Buffer
+		if Run([]string{"setup", "--core-version", "1.0.0-beta.2", flag, "custom"}, &out, &stderr) == 0 {
+			t.Fatal("accepted conflicting selectors")
+		}
+		if !strings.Contains(stderr.String(), "none of the others can be") {
+			t.Fatal(stderr.String())
+		}
+	}
+}
diff --git a/internal/command/testdata/releases/agent.json b/internal/command/testdata/releases/agent.json
new file mode 100644
index 0000000..7dd32bc
--- /dev/null
+++ b/internal/command/testdata/releases/agent.json
@@ -0,0 +1 @@
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Release Notes\n\n\nFirst release, versioned alongside the core it supervises.\n\n### Added\n\n- Supervises the core: starts whatever was installed on a free port, waits for\n  it to answer, and restarts it when it dies, backing off as failures repeat\n- Serves the local view from the binary itself, so it works with no network and\n  cannot drift from the agent serving it: Overview, Graph, Knowledge, Reviews,\n  Skills, Repositories and Settings\n- Asks for a review of a checkout and keeps the answer, so a review has an\n  address that still opens an hour later\n- Proxies `/mcp` to the core, so a coding agent on this machine reaches the same\n  index through the agent it already talks to\n- Reads and writes knowledge, skills, settings and repositories against the\n  index, and browses the filesystem for the folder a person is adding\n\n## Installation\n\n1. 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\ No newline at end of file
diff --git a/internal/command/testdata/releases/cli.json b/internal/command/testdata/releases/cli.json
new file mode 100644
index 0000000..715201e
--- /dev/null
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Release Notes\r\n\r\n\r\nFirst release, versioned alongside the core it reads.\r\n\r\n### Added\r\n\r\n- `sourceant setup` puts the agent and a core on this machine and writes down\r\n  which one, so the agent knows what to start. As a container today, or as a\r\n  Python package once the core is published as one\r\n- An install script, so the command is the only thing anybody fetches by hand\r\n- `sourceant status` says whether the agent and the indexer are running\r\n- `sourceant repos` lists what is indexed here, and `sourceant graph` says what\r\n  the indexer found in one of them\r\n- `sourceant ui` opens the graph in a browser, and says the agent is not running\r\n  rather than opening a browser on an error page\r\n- `--json` on any command prints the agent's own answer, for anything that reads\r\n  rather than looks\r\n- `SOURCEANT_AGENT_URL` names the agent to talk to, and `--agent` overrides it\r\n  for one command\r\n\r\n## Installation\r\n\r\n1. Download the appropriate archive for your platform from the assets below\r\n2. Extract the binary:\r\n   - **Linux/macOS:** `tar -xzf <archive>.tar.gz && chmod +x <binary>`\r\n   - **Windows:** Extract the `.zip` file\r\n3. Move the binary to your PATH (e.g., `/usr/local/bin` on Linux/macOS)\r\n4. Verify the download using `checksums.txt`\r\n"}]
\ No newline at end of file
diff --git a/internal/command/testdata/releases/core.json b/internal/command/testdata/releases/core.json
new file mode 100644
index 0000000..688bd3a
--- /dev/null
+++ b/internal/command/testdata/releases/core.json
@@ -0,0 +1 @@
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Off unless asked for\n- Interfaces for what a deployment provides: which repositories a workspace covers,\n  where its skills are kept, which model it bills, and who is asking. A hosted\n  deployment answers from a database and a personal one from a disk\n- Knowledge can be read across every registered repository at once rather than one\n  at a time\n\n### Changed\n\n- The MCP server is part of the core rather than beside it, and anything able to do\n  something contributes the tools for it\n- A large change is read in parts sized to what a review can take in, rather than to\n  what the model will accept. On a change of a hundred and thirteen files the whole\n  diff yielded between nothing and ten findings and the parts yielded thirty four\n- The parts are read at the same time rather than one after another\n- The reviewer, the folders a workspace covers and the model it bills are resolved\n  through the registry rather than by reaching for a class\n\n### Fixed\n\n- A working checkout is indexed as it is rather than as a commit, and reviews asked\n  for it by commit. The code graph was never reachable from a review of a checkout\n- The claims a suggestion is checked against were optional in the schema a model\n  answers, so it never sent them and nothing was ever checked\n- Names bound at the left margin were recorded by nothing, so a claim that a constant\n  is undefined could not be contradicted by the file defining it\n- Skills are matched on letters rather than on A to Z, so a description written in\n  any other language is no longer split at every accent\n- A page of findings is asked of the database rather than fetched whole and sliced\n- The local API is published on loopback rather than on every interface, and the MCP\n  endpoint refuses a host it does not recognise\n\n\n---\n\n## Deployment\n\nInstall the CLI, and it brings down the rest:\n\n```bash\ncurl -fsSL https://raw.githubusercontent.com/sourceant/cli/main/scripts/install.sh | sh\nsourceant setup\nsourceant ui\n```\n\nSee the [README](README.md) for full setup instructions.\n\n\n## Documentation\n\nSee the [README](README.md) for usage instructions.\n\n## Full Changelog\n\nView the complete version history in [CHANGELOG.md](CHANGELOG.md).\n"}
\ No newline at end of file
diff --git a/internal/install/agent.go b/internal/install/agent.go
index 53c19e9..e454157 100644
--- a/internal/install/agent.go
+++ b/internal/install/agent.go
@@ -4,6 +4,7 @@ import (
 	"archive/tar"
 	"compress/gzip"
 	"encoding/json"
+	"errors"
 	"fmt"
 	"io"
 	"net/http"
@@ -72,27 +73,64 @@ func Get(url string) (io.ReadCloser, error) {
 	}
 	if response.StatusCode != http.StatusOK {
 		response.Body.Close()
-		return nil, fmt.Errorf("%s answered %s", url, response.Status)
+		return nil, &httpError{url: url, status: response.StatusCode}
 	}
 	return response.Body, nil
 }
 
-// LatestAgent asks which version to install when none was named.
+type httpError struct {
+	url    string
+	status int
+}
+
+func (e *httpError) Error() string {
+	return fmt.Sprintf("%s answered HTTP %d", e.url, e.status)
+}
+
 func LatestAgent(get Fetcher) (string, error) {
-	body, err := get(apiBase() + "/latest")
-	if err != nil {
-		return "", err
+	return latestRelease(apiBase(), get)
+}
+
+func LatestCore(get Fetcher) (string, error) {
+	base := os.Getenv("SOURCEANT_CORE_API_BASE")
+	if base == "" {
+		base = "https://api.github.com/repos/" + CoreRepo + "/releases"
 	}
-	defer body.Close()
-	var release struct {
+	return latestRelease(base, get)
+}
+
+func latestRelease(base string, get Fetcher) (string, error) {
+	type release struct {
 		Tag string `json:"tag_name"`
 	}
-	if err := json.NewDecoder(body).Decode(&release); err != nil {
-		return "", err
+	body, err := get(base + "/latest")
+	var selected release
+	if err != nil {
+		var status *httpError
+		if !errors.As(err, &status) || status.status != http.StatusNotFound {
+			return "", err
+		}
+		body, err = get(base + "?per_page=1")
+		if err != nil {
+			return "", err
+		}
+		defer func() { _ = body.Close() }()
+		var releases []release
+		if err := json.NewDecoder(body).Decode(&releases); err != nil {
+			return "", err
+		}
+		if len(releases) > 0 {
+			selected = releases[0]
+		}
+	} else {
+		defer func() { _ = body.Close() }()
+		if err := json.NewDecoder(body).Decode(&selected); err != nil {
+			return "", err
+		}
 	}
-	tag := strings.TrimPrefix(release.Tag, "v")
+	tag := strings.TrimPrefix(selected.Tag, "v")
 	if tag == "" {
-		return "", fmt.Errorf("%s names no latest release", AgentRepo)
+		return "", fmt.Errorf("%s names no published release", base)
 	}
 	return tag, nil
 }
@@ -118,6 +156,8 @@ func InstallAgent(version string, get Fetcher, out io.Writer) (string, error) {
 		}
 	}
 
+	version = strings.TrimPrefix(version, "v")
+
 	say(out, "Fetching %s %s for %s.\n", AgentName, version, platform)
 	body, err := get(AgentURL(version, platform))
 	if err != nil {
diff --git a/internal/install/install.go b/internal/install/install.go
index d32558d..ead793d 100644
--- a/internal/install/install.go
+++ b/internal/install/install.go
@@ -158,6 +158,9 @@ func installDocker(opts Options, run Runner) (Config, error) {
 	image := opts.Image
 	if image == "" {
 		image = DefaultImage
+		if opts.Version != "" && opts.Version != "latest" {
+			image = "ghcr.io/sourceant/sourceant:v" + strings.TrimPrefix(opts.Version, "v")
+		}
 	}
 	if _, err := run("docker", "version", "--format", "{{.Server.Version}}"); err != nil {
 		return Config{}, errors.New("docker is not running here. Start it, or install the python runtime instead")
@@ -197,7 +200,15 @@ func installDocker(opts Options, run Runner) (Config, error) {
 func installPython(opts Options, run Runner) (Config, error) {
 	from := opts.From
 	if from == "" {
-		from = CoreWheel(opts.Version)
+		version := strings.TrimPrefix(opts.Version, "v")
+		if version == "" || version == "latest" {
+			var err error
+			version, err = LatestCore(Get)
+			if err != nil {
+				return Config{}, fmt.Errorf("could not tell which core to install: %w", err)
+			}
+		}
+		from = CoreWheel(version)
 	}
 	python, err := exec.LookPath("python3")
 	if err != nil {
diff --git a/scripts/install.sh b/scripts/install.sh
index bd5ea72..0e38f1b 100755
--- a/scripts/install.sh
+++ b/scripts/install.sh
@@ -39,10 +39,20 @@ resolve() {
         printf '%s' "${VERSION#v}"
         return
     fi
-    # The tag, read without jq so this works on a machine with nothing on it.
-    tag=$(curl -fsSL "$API_BASE/latest" |
+    status=$(curl -sSL -w '\n%{http_code}' "$API_BASE/latest") ||
+        die "could not reach $API_BASE/latest"
+    code=$(printf '%s\n' "$status" | tail -1)
+    case "$code" in
+        200) ;;
+        404)
+            status=$(curl -fsSL "$API_BASE?per_page=1") ||
+                die "could not fetch releases from $API_BASE"
+            ;;
+        *) die "release lookup returned HTTP $code from $API_BASE/latest" ;;
+    esac
+    tag=$(printf '%s\n' "$status" |
         sed -n 's/.*"tag_name" *: *"\([^"]*\)".*/\1/p' | head -1)
-    [ -n "$tag" ] || die "could not tell which version is latest"
+    [ -n "$tag" ] || die "no published release found; set SOURCEANT_VERSION to a release version"
     printf '%s' "${tag#v}"
 }