Keep every composition the engine applied on the machine, so a module whose composition the bus no longer keeps runs as applied and is never composed as nothing (issue 774)

On novox on 2026-10-29 at 07:54 UTC the kept declaration was retired and the node's own composition was in no bucket.
The composer's first pass reads what runs before the agent reads any have (the agent waits for the composer's caught,
sent after that pass), so the node's own was composed with its folded modules running nothing, and the bus server and
four held modules were removed.

- Quick fix: read the node's own have in loadHad too. It still waits for the composer's first pass, and still finds
  nothing when the bucket no longer keeps the composition the have names.
- Thorough fix, chosen: the engine keeps each composition it applied (the node's own too) in `applied/` beside its
  state, 0600. The agent reads it at Run's start, before any watch, as what runs ahead of the bucket and the kept
  declaration. A have naming another running composition wins. An apply keeps; a removal forgets.

Test: a case in TestEverythingIsWhatTheAgentRunsAndWhatIsKeptForTheRest (no new test function). It fails on L3's
engine 4f9227a (0 compositions at the first own composition) and passes here.

cmd/mesh-host/applied_store.go

@@ -0,0 +1,97 @@
+package main
+
+import (
+	"errors"
+	"fmt"
+	"os"
+	"path/filepath"
+	"regexp"
+	"strings"
+)
+
+// appliedStore keeps every composition the agent applied, one file per module (the node's own as `node.json`), in the
+// directory `applied` beside the node's state (agent.Env.Applied, issue 774). It is the machine's own record of what runs:
+// read at the agent's start before anything is watched, so the node never composes its own as if a module it runs ran
+// nothing because the bucket no longer keeps that composition or the kept declaration is retired. Files are 0600 in a
+// 0700 directory: a composition carries values sealed to this machine.
+type appliedStore struct{ dir string }
+
+func appliedStoreFor(statePath string) appliedStore {
+	return appliedStore{dir: filepath.Join(filepath.Dir(statePath), "applied")}
+}
+
+// appliedName is a module name the store takes as a file name: a catalogue module's or the node's own, never a path.
+var appliedName = regexp.MustCompile(`^[a-z0-9][a-z0-9._-]*$`)
+
+func (s appliedStore) path(module string) (string, error) {
+	if !appliedName.MatchString(module) || strings.Contains(module, "..") {
+		return "", fmt.Errorf("%q is not a module name the applied store takes", module)
+	}
+	return filepath.Join(s.dir, module+".json"), nil
+}
+
+func (s appliedStore) Load() (map[string][]byte, error) {
+	entries, err := os.ReadDir(s.dir)
+	if errors.Is(err, os.ErrNotExist) {
+		return nil, nil
+	}
+	if err != nil {
+		return nil, err
+	}
+	out := map[string][]byte{}
+	var errs []error
+	for _, e := range entries {
+		module, ok := strings.CutSuffix(e.Name(), ".json")
+		if !ok || e.IsDir() || !appliedName.MatchString(module) {
+			continue
+		}
+		raw, err := os.ReadFile(filepath.Join(s.dir, e.Name()))
+		if err != nil {
+			errs = append(errs, err)
+			continue
+		}
+		out[module] = raw
+	}
+	return out, errors.Join(errs...)
+}
+
+func (s appliedStore) Keep(module string, raw []byte) error {
+	path, err := s.path(module)
+	if err != nil {
+		return err
+	}
+	if was, err := os.ReadFile(path); err == nil && string(was) == string(raw) {
+		return nil
+	}
+	if err := os.MkdirAll(s.dir, 0o700); err != nil {
+		return err
+	}
+	tmp, err := os.CreateTemp(s.dir, "."+module+".*")
+	if err != nil {
+		return err
+	}
+	defer os.Remove(tmp.Name())
+	if _, err := tmp.Write(raw); err != nil {
+		tmp.Close()
+		return err
+	}
+	if err := tmp.Sync(); err != nil {
+		tmp.Close()
+		return err
+	}
+	if err := tmp.Close(); err != nil {
+		return err
+	}
+	return os.Rename(tmp.Name(), path)
+}
+
+func (s appliedStore) Drop(module string) error {
+	path, err := s.path(module)
+	if err != nil {
+		return err
+	}
+	if err := os.Remove(path); err != nil && !errors.Is(err, os.ErrNotExist) {
+		return err
+	}
+	return nil
+}

cmd/mesh-host/nodeagent.go

@@ -494,7 +494,10 @@ func nodeAgent(ctx context.Context, opts options, signer ed25519.PublicKey, trus
 			// The same kept declaration's filled paths, so a module still running from it keeps its files filled.
 			KeptFilled: func() map[string][]string { _, filled := kept(); return filled },
 			Recorded:   recordedIn(opts.state, say),
-			Inactive:   inactiveIn(&liveness.Exec{Run: apply.ExecRunner, System: builtFor}, heldBy(apply.WindowsIn(filepath.Dir(opts.state)))),
+			// What this engine applied, kept on the machine and read at the start, so what runs is known before the node
+			// composes its own (issue 774).
+			Applied:  appliedStoreFor(opts.state),
+			Inactive: inactiveIn(&liveness.Exec{Run: apply.ExecRunner, System: builtFor}, heldBy(apply.WindowsIn(filepath.Dir(opts.state)))),
 			Revisions: func(ctx context.Context, key string) ([]agent.Update, error) {
 				got, err := session.KVHistory(ctx, composedBucket, key)
 				if err != nil {