Look at what a container mounts directly, accept a pre-upgrade label, and write the genesis secret without a newline

Review of the first cut found four things.

A directory mounted into a container is no longer looked inside, not even
for the files this host wrote there. The controller records every
provider's received and contributions file as a plain file under a mounted
directory, so folding those in would have recreated the route proxy — which
re-reads its routes live, by design — on every route change, and killed
every provisioner sidecar, which polls what it receives, mid-reconcile on
every grant. Whether a service reads a file under its directory once or
watches it is the service's; restart-on is how a module says "once", and it
stays the opt-in. Env-files and files mounted directly remain by content.

Genesis wrote the superuser secret as `value\n`; `secret accept` strips the
line ending by design, so the postgres module declared `value` — and with
a mounted file's content in the spec, phase three would have recreated the
store it meant to adopt in place, with the temporary control plane
connected to it. Genesis now writes the value alone. readCredentialFile
tolerated both endings already. Pinned with the bytes the genesis code
path writes, then the module's declaration of the same container: it must
reconcile.

A container carrying a label from before the host folded in what it reads
is accepted rather than recreated, when that label matches the spec as it
used to be computed: what it reads is recorded then, a change is caught
from that record from the next apply on, and the label is renewed at the
next genuine recreate. Recreating them all would have been a restart storm
across the mesh in declaration order, the store first. The trade-off is
stated in the code: a container already stale at upgrade time is not
caught, and could not have been either way.

The record of what a container read is looked up by its name when its
declared id has none — the bundle's `store` becomes `postgres.server` for
the same container — so a change on the day it is adopted still names the
file. The by-target lookup takes the most recently applied record, since
the bundle's record for the same target is never removed by the mesh's.

novox/hq 04-ISSUES/103

internal/apply/apply.go

@@ -52,6 +52,9 @@ type Outcome struct {
 	wrote string
 	// into is what a file written into held before the mesh's keys (novox/hq ADR 0102).
 	into *store.Into
+	// reads is, for a container, the digest of each file it was created reading, by path — so
+	// the next apply can say which one changed (novox/hq 04-ISSUES/103).
+	reads map[string]string
 }
 
 // Report is what an apply did, in the order it did it.
@@ -266,9 +269,16 @@ func ApplyKeeping(
 	// machine reports success, and what is inside is using a credential the mesh has replaced
 	// (novox/hq 04-ISSUES/045). Folding these into the container's spec makes the comparison a
 	// standing one instead.
-	declares := map[string]string{}
+	//
+	// And what each file a container reads at creation holds — its env-files and what is mounted
+	// into it — by the digest this host recorded when it wrote the file, read from `known` as it
+	// stands when the container is reached, so a file rewritten earlier in this same apply is
+	// already the new one (novox/hq 04-ISSUES/103). That needs the file applied before the
+	// container, which is the declared order; a container declared ahead of its file sees the
+	// change one apply late, and never misses it.
+	in := inputs{declares: map[string]string{}, known: &known}
 	for _, resource := range d.Resources {
-		declares[resource.Identity()] = declaredDigest(resource)
+		in.declares[resource.Identity()] = declaredDigest(resource)
 	}
 
 	// Everything is attempted, and every failure is reported.
@@ -340,7 +350,7 @@ func ApplyKeeping(
 				!known.Recorded(string(declaration.TypeFile), f.Path) {
 				keepFound = keep
 			}
-			outcome, err = applyOne(ctx, sys, resource, run, changed, declares, was, unseal, keepFound)
+			outcome, err = applyOne(ctx, sys, resource, run, changed, in, was, unseal, keepFound)
 		}
 		if err != nil {
 			failed := &Error{Resource: resource.Identity(), Err: err, Done: report}
@@ -386,6 +396,7 @@ func ApplyKeeping(
 			Target: outcome.Target, AppliedAt: time.Now().UTC(),
 			Wrote: outcome.wrote,
 			Into:  outcome.into,
+			Reads: outcome.reads,
 			Holds: holds(resource),
 		})
 		// Its module has been taken, and what was held for it is now the mesh's.
@@ -396,7 +407,14 @@ func ApplyKeeping(
 		report.Outcomes = append(report.Outcomes, outcome)
 		if outcome.Action != "unchanged" {
 			changed[resource.Identity()] = true
-			log(fmt.Sprintf("  %s %s (%s)", outcome.Action, outcome.ID, outcome.Target))
+			// With the detail, when there is one: "updated app" says a container was replaced;
+			// which file made that happen is what somebody reading the log at the time needs
+			// (novox/hq 04-ISSUES/103).
+			line := fmt.Sprintf("  %s %s (%s)", outcome.Action, outcome.ID, outcome.Target)
+			if outcome.Detail != "" {
+				line += ": " + outcome.Detail
+			}
+			log(line)
 		}
 	}
 
@@ -440,7 +458,7 @@ const guardPrefix = declaration.AdoptionPrefix + "guard"
 type Unseal func(sealed string) ([]byte, error)
 
 func applyOne(ctx context.Context, sys system.System, r declaration.Resource, run Runner,
-	changed map[string]bool, declares map[string]string, previous store.Applied,
+	changed map[string]bool, in inputs, previous store.Applied,
 	unseal Unseal, keepFound Keep) (Outcome, error) {
 	switch res := r.(type) {
 	case *declaration.Directory:
@@ -452,7 +470,7 @@ func applyOne(ctx context.Context, sys system.System, r declaration.Resource, ru
 	case *declaration.Package:
 		return applyPackage(ctx, sys, res, run)
 	case *declaration.Container:
-		return applyContainer(ctx, res, run, changed, declares, previous)
+		return applyContainer(ctx, res, run, changed, in, previous)
 	case *declaration.User:
 		return applyUser(ctx, sys, res, run)
 	case *declaration.Archive:
@@ -1129,9 +1147,96 @@ const (
 	idLabel   = "mesh-host.id"
 )
 
+// inputs is what a container takes in when it is created beyond its own declaration: what each
+// resource it names under restart-on currently declares, and what the files it reads hold.
+type inputs struct {
+	// declares is each resource's declared digest, by id (declaredDigest).
+	declares map[string]string
+	// known is the node's state as it stands when the container is reached — so a file applied
+	// earlier in the same pass is already its new self. Nil where nothing was written: a test,
+	// or a scheduled fire, which reads no file at creation.
+	known *store.State
+}
+
+// fileDigest is what a file the container reads holds, by digest.
+//
+// **What this host wrote when it has a record of writing it, and what is on disk when it has
+// not.** The record is preferred because it is what the host means by the file: a seed created
+// once digests as the seed, not as whatever the service has grown in it, and a file written into
+// digests as the mesh's keys, not the machine's (novox/hq ADR 0102). A file the host never wrote
+// — an env-file a predecessor left, the superuser secret genesis writes before any declaration
+// names it — is read, so the digest is the same one the host records when it later writes the
+// same bytes there, and adopting a running store in place stays a reconcile rather than a
+// recreate (bootstrap phase three; genesis writes the value with no line ending for exactly this
+// reason). Empty when there is nothing readable there: the runtime refuses an absent env-file
+// itself, with a better message than this could give.
+func (in inputs) fileDigest(path string) string {
+	if in.known != nil {
+		if f, recorded := in.known.At(string(declaration.TypeFile), path); recorded {
+			return f.Wrote
+		}
+	}
+	info, err := os.Stat(path)
+	if err != nil || !info.Mode().IsRegular() {
+		return ""
+	}
+	content, err := os.ReadFile(path)
+	if err != nil {
+		return ""
+	}
+	return digestOf(string(content))
+}
+
+// reads is every file a running container takes in when it is created, by path and digest
+// (novox/hq 04-ISSUES/103).
+//
+//   - every env-file: the runtime reads it once, at create, and `docker restart` hands the
+//     container the same environment it had.
+//   - a file bind-mounted into it, DIRECTLY, by its content: a secret, a credential file.
+//
+// **A directory bind-mounted into it is not looked inside**, not even for the files this host
+// wrote there. What a service reads out of a mounted directory, and when, is the service's
+// business: the route proxy re-reads its routes file live and would be recreated on every route
+// change; a provisioner sidecar polls what it receives every few seconds and would be killed
+// mid-reconcile on every grant. A module whose container does read such a file once, at start,
+// says so with restart-on — that is what the field is for, and it stays the opt-in.
+//
+// A step is not here either: a run-once or scheduled container reads its files when it runs, and
+// runs fresh each time. Only a container that stays running holds what it read.
+func (in inputs) reads(r *declaration.Container) map[string]string {
+	if r.RunOnce || r.Schedule != "" {
+		return nil
+	}
+	out := map[string]string{}
+	for _, path := range r.EnvFile {
+		out[path] = in.fileDigest(path)
+	}
+	for _, v := range r.Volumes {
+		src := mountSource(v)
+		if !strings.HasPrefix(src, "/") {
+			continue // a named volume: the runtime's, holding data
+		}
+		// fileDigest is empty for a directory, and for anything else that is not a regular file.
+		if digest := in.fileDigest(src); digest != "" {
+			out[src] = digest
+		}
+	}
+	if len(out) == 0 {
+		return nil
+	}
+	return out
+}
+
 // containerSpec is the identity of a declared container: everything that, if changed, means
 // the running container is no longer what was asked for.
-func containerSpec(r *declaration.Container, declares map[string]string) string {
+func containerSpec(r *declaration.Container, in inputs) string {
+	return containerSpecReading(r, in.declares, in.reads(r))
+}
+
+// containerSpecReading is containerSpec with what the container reads already read — so an
+// applier that also records those digests reads each file once, and the label and the record
+// cannot disagree about a file that moved between two reads.
+func containerSpecReading(r *declaration.Container, declares, reads map[string]string) string {
 	keys := make([]string, 0, len(r.Env))
 	for k := range r.Env {
 		keys = append(keys, k)
@@ -1171,6 +1276,15 @@ func containerSpec(r *declaration.Container, declares map[string]string) string
 	for _, id := range depends {
 		b.WriteString("reads " + id + "=" + declares[id] + "\n")
 	}
+	// And what the files it reads at creation hold — not only their paths, which `volume` and the
+	// env-file arguments already name. The spec named the env-file's path and not its content,
+	// so the host rewrote two environment files with the store's new port and left both
+	// containers running with the old one, healthy-looking, until they answered 502 (novox/hq
+	// 04-ISSUES/103). Added only when there is something read, so a container that reads nothing
+	// keeps the digest it had.
+	for _, path := range sortedKeys(reads) {
+		b.WriteString("file " + path + "=" + reads[path] + "\n")
+	}
 	return fmt.Sprintf("%x", sha256.Sum256([]byte(b.String())))
 }
 
@@ -1236,9 +1350,12 @@ func applyNetwork(ctx context.Context, r *declaration.Network, run Runner) (Outc
 }
 
 func applyContainer(ctx context.Context, r *declaration.Container, run Runner,
-	changed map[string]bool, declares map[string]string, previous store.Applied) (Outcome, error) {
+	changed map[string]bool, in inputs, previous store.Applied) (Outcome, error) {
 	out := begin(r)
-	want := containerSpec(r, declares)
+	// Read once, so the spec and the record agree on what was read even if a file moves under them.
+	reads := in.reads(r)
+	want := containerSpecReading(r, in.declares, reads)
+	out.reads = reads
 
 	cri, err := containerRuntime(ctx, run)
 	if err != nil {
@@ -1279,8 +1396,42 @@ func applyContainer(ctx context.Context, r *declaration.Container, run Runner,
 	// already has.
 	reasons := restartedBy(r.RestartOn, changed)
 
+	// What this container was created reading, as last recorded. By its declared id first, and by
+	// its NAME when that id has no record: the bundle's `store` becomes the postgres module's
+	// `postgres.server`, the same container under a new id, and a file change on the day it is
+	// adopted is a real change with a real record — under the old id.
+	wasReading := previous.Reads
+	if previous.ID == "" && in.known != nil {
+		if byName, ok := in.known.At(string(declaration.TypeContainer), r.Name); ok {
+			wasReading = byName.Reads
+		}
+	}
+
+	// Which of the files it reads no longer hold what it was created reading. The spec label says
+	// only that SOMETHING moved; the record of what was read says what — and that is the line a
+	// person needs when a service went stale without a word (novox/hq 04-ISSUES/103).
+	var changedFiles []string
+	for _, path := range sortedKeys(wasReading) {
+		if now, still := reads[path]; still && now != wasReading[path] {
+			changedFiles = append(changedFiles, path)
+		}
+	}
+
+	// **A container labelled before the host folded in what it reads is accepted, not recreated.**
+	//
+	// Its label is the spec without the file lines. Recreating every such container on the first
+	// apply after the host upgraded would be a restart storm across the mesh in declaration order —
+	// the store first, under everything that uses it. So a label that matches the spec as it used
+	// to be computed is taken as current: what it reads is recorded now, and from the next apply
+	// on a changed file is caught by that record; the label itself is rewritten at the next
+	// genuine recreate. The trade-off, stated: a container that was ALREADY stale when the host
+	// upgraded — created against a file that has since changed — is not caught by this, and could
+	// not be by the alternative either, which recreates it without knowing whether it needed to.
+	legacy := len(reads) > 0 && before.Spec == containerSpecReading(r, in.declares, nil) &&
+		(wasReading == nil || sameReads(wasReading, reads))
+
 	switch {
-	case existed && before.Spec == want && before.Running && len(reasons) == 0:
+	case existed && (before.Spec == want || legacy) && before.Running && len(reasons) == 0:
 		out.Action = "unchanged"
 		return out, nil
 	case existed:
@@ -1340,9 +1491,15 @@ func applyContainer(ctx context.Context, r *declaration.Container, run Runner,
 	out.Action = "created"
 	if existed {
 		out.Action = "updated"
-		if len(reasons) > 0 {
+		switch {
+		case len(changedFiles) > 0:
+			out.Detail = "recreated: " + strings.Join(changedFiles, ", ") + " changed"
+			if len(reasons) > 0 {
+				out.Detail += "; and to pick up " + strings.Join(reasons, ", ")
+			}
+		case len(reasons) > 0:
 			out.Detail = "recreated to pick up " + strings.Join(reasons, ", ")
-		} else {
+		default:
 			out.Detail = "replaced; a container's configuration is fixed when it is created"
 		}
 	}
@@ -1510,6 +1667,20 @@ func restartedBy(restartOn []string, changed map[string]bool) []string {
 	return which
 }
 
+// sameReads is whether two records of what a container reads name the same files holding the
+// same content — a file added, dropped or changed makes them differ.
+func sameReads(a, b map[string]string) bool {
+	if len(a) != len(b) {
+		return false
+	}
+	for path, digest := range a {
+		if b[path] != digest {
+			return false
+		}
+	}
+	return true
+}
+
 func sortedKeys(m map[string]string) []string {
 	keys := make([]string, 0, len(m))
 	for k := range m {

internal/apply/apply_test.go

@@ -666,7 +666,7 @@ func TestAContainerWhoseDeclarationChangedIsReplaced(t *testing.T) {
 	d := parseTrusted(t, `{"declaration":1,"resources":[
 	  {"id":"store","type":"container","name":"store","image":"`+pinned+`","env":{"PGDATA":"/data"}}
 	]}`)
-	want := containerSpec(d.Resources[0].(*declaration.Container), nil)
+	want := containerSpec(d.Resources[0].(*declaration.Container), inputs{})
 
 	var removed, created bool
 	run := func(ctx context.Context, name string, args ...string) (string, error) {
@@ -704,7 +704,7 @@ func TestAContainerThatMatchesIsLeftAlone(t *testing.T) {
 	d := parseTrusted(t, `{"declaration":1,"resources":[
 	  {"id":"store","type":"container","name":"store","image":"`+pinned+`","env":{"PGDATA":"/data"}}
 	]}`)
-	spec := containerSpec(d.Resources[0].(*declaration.Container), nil)
+	spec := containerSpec(d.Resources[0].(*declaration.Container), inputs{})
 
 	var touched bool
 	run := func(ctx context.Context, name string, args ...string) (string, error) {
@@ -748,8 +748,8 @@ func TestAContainerIsRecreatedWhenARestartOnResourceChanged(t *testing.T) {
 	// what a container reads is part of what it is, so the old content yields a different spec.
 	was := map[string]string{"config": declaredDigest(&declaration.File{Content: "{\"token\":\"old\"}\n"})}
 	now := map[string]string{"config": declaredDigest(d.Resources[0].(*declaration.File))}
-	stale := containerSpec(d.Resources[1].(*declaration.Container), was)
-	fresh := containerSpec(d.Resources[1].(*declaration.Container), now)
+	stale := containerSpec(d.Resources[1].(*declaration.Container), inputs{declares: was})
+	fresh := containerSpec(d.Resources[1].(*declaration.Container), inputs{declares: now})
 
 	var removed, created bool
 	run := func(ctx context.Context, name string, args ...string) (string, error) {
@@ -1538,8 +1538,8 @@ func TestAContainerStaleFromAnEarlierApplyIsReplaced(t *testing.T) {
 	// The container was created when the file said something else.
 	was := map[string]string{"env": declaredDigest(&declaration.File{Content: "PASSWORD=old\n"})}
 	now := map[string]string{"env": declaredDigest(d.Resources[0].(*declaration.File))}
-	stale := containerSpec(d.Resources[1].(*declaration.Container), was)
-	fresh := containerSpec(d.Resources[1].(*declaration.Container), now)
+	stale := containerSpec(d.Resources[1].(*declaration.Container), inputs{declares: was})
+	fresh := containerSpec(d.Resources[1].(*declaration.Container), inputs{declares: now})
 
 	var removed, created bool
 	run := func(ctx context.Context, name string, args ...string) (string, error) {

internal/apply/reads_test.go

@@ -0,0 +1,316 @@
+package apply
+
+import (
+	"context"
+	"os"
+	"path/filepath"
+	"strings"
+	"testing"
+
+	"github.com/novox/mesh-host/internal/declaration"
+	"github.com/novox/mesh-host/internal/store"
+)
+
+// Defends novox/hq 04-ISSUES/103: a container is recreated when the CONTENT of a file it reads at
+// creation changes, not only when its path does. A container takes its env-file and its mounted
+// files in once, when it is created; `docker restart` hands it the same environment again, so
+// only a recreate carries a rewritten file into the process.
+//
+// The runtime here is the `machine` fake: it keeps the spec label the host gave a container and
+// hands it back on inspect, so the comparison under test is the one the host really makes,
+// against what it really wrote — not against a spec a test imagined.
+
+func applyCarried(t *testing.T, d *declaration.Declaration, known store.State, m *machine,
+	log func(string)) (Report, store.State) {
+	t.Helper()
+	report, state, err := Apply(context.Background(), archHost(t), d, known, store.OriginCarried, m.run, log, nil)
+	if err != nil {
+		t.Fatalf("apply failed: %v", err)
+	}
+	return report, state
+}
+
+func TestAContainerIsRecreatedWhenItsEnvFileChanged(t *testing.T) {
+	// The night of the issue: the store was given a new port, the host rewrote the forge's
+	// environment file with it — and left the forge running with the old one.
+	dir := t.TempDir()
+	env := filepath.Join(dir, "forge.env")
+	declare := func(port string) *declaration.Declaration {
+		return parseTrusted(t, `{"declaration":1,"resources":[
+		  {"id":"forge.env","type":"file","path":"`+env+`","content":"DATABASE_PORT=`+port+`\n","mode":"0600"},
+		  {"id":"forge.server","type":"container","name":"forge","image":"`+pinned+`","env-file":["`+env+`"]}
+		]}`)
+	}
+	m := &machine{containers: map[string]*fakeContainer{}}
+	var logged []string
+	log := func(line string) { logged = append(logged, line) }
+
+	report, state := applyCarried(t, declare("5432"), store.State{}, m, log)
+	if o := outcomeOf(report, "forge.server"); o.Action != "created" {
+		t.Fatalf("the container was not created: %+v", report.Outcomes)
+	}
+
+	// The store moved. The file is rewritten in this apply, before the container is reached, and
+	// the container must follow it in the same pass.
+	m.asked, logged = nil, nil
+	report, state = applyCarried(t, declare("5433"), state, m, log)
+	if !m.removed("forge") || !m.did("docker run") {
+		t.Fatalf("the container kept running with the old environment after its env-file changed: %v", m.asked)
+	}
+	o := outcomeOf(report, "forge.server")
+	if o.Action != "updated" || o.Detail != "recreated: "+env+" changed" {
+		t.Errorf("the recreate did not say which file changed: %+v", o)
+	}
+	var said bool
+	for _, line := range logged {
+		if strings.Contains(line, "updated forge.server") && strings.Contains(line, "recreated: "+env+" changed") {
+			said = true
+		}
+	}
+	if !said {
+		t.Errorf("the log did not say which file made the container recreate: %q", logged)
+	}
+
+	// And with nothing moved, it is left alone: content is part of the identity, not a tripwire.
+	m.asked = nil
+	report, _ = applyCarried(t, declare("5433"), state, m, log)
+	if m.did("docker rm") || m.did("docker run") || report.Changed() {
+		t.Errorf("a container whose env-file did not change was recreated: %v %+v", m.asked, report.Outcomes)
+	}
+}
+
+func TestAnEnvFileTheHostDidNotWriteIsStillReadForWhatItHolds(t *testing.T) {
+	// The host has no record of this file — a predecessor left it, or something else on the
+	// machine maintains it — and the container still reads it once. Its content is read from the
+	// disk, so a change is a recreate exactly as for a file the host wrote.
+	dir := t.TempDir()
+	env := filepath.Join(dir, "app.env")
+	if err := os.WriteFile(env, []byte("TOKEN=old\n"), 0o600); err != nil {
+		t.Fatal(err)
+	}
+	d := parseTrusted(t, `{"declaration":1,"resources":[
+	  {"id":"app.server","type":"container","name":"app","image":"`+pinned+`","env-file":["`+env+`"]}
+	]}`)
+	m := &machine{containers: map[string]*fakeContainer{}}
+	_, state := applyCarried(t, d, store.State{}, m, nil)
+
+	if err := os.WriteFile(env, []byte("TOKEN=new\n"), 0o600); err != nil {
+		t.Fatal(err)
+	}
+	m.asked = nil
+	report, _ := applyCarried(t, d, state, m, nil)
+	if !m.removed("app") || !m.did("docker run") {
+		t.Fatalf("a container reading an env-file the host did not write was not recreated when it changed: %v", m.asked)
+	}
+	if o := outcomeOf(report, "app.server"); o.Detail != "recreated: "+env+" changed" {
+		t.Errorf("the recreate did not name the file: %+v", o)
+	}
+}
+
+func TestAContainerIsRecreatedWhenAMountedSecretChanged(t *testing.T) {
+	// A rotated credential has the same shape as a moved port: the host writes the file the
+	// container mounts, and the process holds the value it was created with.
+	dir := t.TempDir()
+	secret := filepath.Join(dir, "db.secret")
+	declare := func(value string) *declaration.Declaration {
+		return parseTrusted(t, `{"declaration":1,"resources":[
+		  {"id":"app.secret","type":"file","path":"`+secret+`","content":"`+value+`","mode":"0600"},
+		  {"id":"app.server","type":"container","name":"app","image":"`+pinned+`",
+		   "volumes":["`+secret+`:/run/secrets/db:ro"]}
+		]}`)
+	}
+	m := &machine{containers: map[string]*fakeContainer{}}
+	_, state := applyCarried(t, declare("hunter2"), store.State{}, m, nil)
+
+	m.asked = nil
+	report, _ := applyCarried(t, declare("correct-horse-battery-staple"), state, m, nil)
+	if !m.removed("app") || !m.did("docker run") {
+		t.Fatalf("the container kept the secret it was created with after the mounted file changed: %v", m.asked)
+	}
+	if o := outcomeOf(report, "app.server"); o.Action != "updated" || o.Detail != "recreated: "+secret+" changed" {
+		t.Errorf("the recreate did not say which file changed: %+v", o)
+	}
+}
+
+func TestAMountedDirectoryIsNotLookedInside(t *testing.T) {
+	// A bind-mounted directory is not part of what a container is — not the data the service
+	// grows in it, and not the files the host itself writes there either. Whether a service reads
+	// a file under its directory once at start or watches it live is the service's business: the
+	// route proxy re-reads its routes live, a provisioner sidecar polls what it receives every few
+	// seconds, and recreating either for a file the host rewrote would kill them for nothing. A
+	// module whose container does read such a file once says so with restart-on, which stays the
+	// opt-in.
+	dir := t.TempDir()
+	state := filepath.Join(dir, "state")
+	config := filepath.Join(state, "config.toml")
+	declare := func(level, restartOn string) *declaration.Declaration {
+		return parseTrusted(t, `{"declaration":1,"resources":[
+		  {"id":"app.state","type":"directory","path":"`+state+`"},
+		  {"id":"app.config","type":"file","path":"`+config+`","content":"level = \"`+level+`\"\n"},
+		  {"id":"app.server","type":"container","name":"app","image":"`+pinned+`",
+		   "volumes":["`+state+`:/var/lib/app"]`+restartOn+`}
+		]}`)
+	}
+	m := &machine{containers: map[string]*fakeContainer{}}
+	_, known := applyCarried(t, declare("info", ""), store.State{}, m, nil)
+
+	// The service grows its data in the directory it was given.
+	if err := os.WriteFile(filepath.Join(state, "app.db"), []byte("rows"), 0o600); err != nil {
+		t.Fatal(err)
+	}
+	if err := os.MkdirAll(filepath.Join(state, "cache"), 0o700); err != nil {
+		t.Fatal(err)
+	}
+	if err := os.WriteFile(filepath.Join(state, "cache", "index"), []byte("entries"), 0o600); err != nil {
+		t.Fatal(err)
+	}
+	m.asked = nil
+	report, known := applyCarried(t, declare("info", ""), known, m, nil)
+	if m.did("docker rm") || m.did("docker run") || report.Changed() {
+		t.Errorf("a container was recreated for data its service wrote in a mounted directory: %v %+v",
+			m.asked, report.Outcomes)
+	}
+
+	// The host rewrites its own file under the same directory: still not a reason. The container
+	// did not name it.
+	m.asked = nil
+	report, known = applyCarried(t, declare("debug", ""), known, m, nil)
+	if m.did("docker rm") || m.did("docker run") {
+		t.Errorf("a container was recreated for a file under a mounted directory it did not name: %v", m.asked)
+	}
+	if o := outcomeOf(report, "app.config"); o.Action != "updated" {
+		t.Fatalf("the config was not rewritten: %+v", o)
+	}
+
+	// Naming it is what makes it a reason, as before this change.
+	m.asked = nil
+	report, _ = applyCarried(t, declare("trace", `,"restart-on":["app.config"]`), known, m, nil)
+	if !m.removed("app") || !m.did("docker run") {
+		t.Fatalf("a container naming a rewritten file under its mount was not recreated: %v", m.asked)
+	}
+	if o := outcomeOf(report, "app.server"); !strings.Contains(o.Detail, "app.config") {
+		t.Errorf("the recreate did not name why: %+v", o)
+	}
+}
+
+func TestAContainerLabelledBeforeTheHostReadItsFilesIsAcceptedNotRecreated(t *testing.T) {
+	// The first apply after the host upgrades finds every container carrying a label computed
+	// without the file lines. Recreating them all would be a restart storm across the mesh in
+	// declaration order, the store first. A label that matches the spec as it used to be computed
+	// is accepted: what the container reads is recorded now, and from then on a change is caught.
+	dir := t.TempDir()
+	env := filepath.Join(dir, "forge.env")
+	declare := func(port string) *declaration.Declaration {
+		return parseTrusted(t, `{"declaration":1,"resources":[
+		  {"id":"forge.env","type":"file","path":"`+env+`","content":"DATABASE_PORT=`+port+`\n","mode":"0600"},
+		  {"id":"forge.server","type":"container","name":"forge","image":"`+pinned+`","env-file":["`+env+`"]}
+		]}`)
+	}
+	// The machine as the previous host left it: the file written and recorded, the container up
+	// under the label that host computed — the spec with nothing about the file's content.
+	if err := os.WriteFile(env, []byte("DATABASE_PORT=5432\n"), 0o600); err != nil {
+		t.Fatal(err)
+	}
+	d := declare("5432")
+	legacy := containerSpecReading(d.Resources[1].(*declaration.Container), nil, nil)
+	known := store.State{}
+	known.Record(store.Applied{ID: "forge.env", Type: "file", Origin: store.OriginCarried, Target: env,
+		Wrote: digestOf("DATABASE_PORT=5432\n")})
+	known.Record(store.Applied{ID: "forge.server", Type: "container", Origin: store.OriginCarried, Target: "forge"})
+	m := &machine{containers: map[string]*fakeContainer{"forge": {id: "made-by-host", running: true, spec: legacy}}}
+
+	report, known := applyCarried(t, d, known, m, nil)
+	if m.did("docker rm") || m.did("docker run") || report.Changed() {
+		t.Fatalf("a container labelled by the previous host was recreated on upgrade: %v %+v", m.asked, report.Outcomes)
+	}
+	if got, _ := known.Find("forge.server"); got.Reads[env] != digestOf("DATABASE_PORT=5432\n") {
+		t.Fatalf("what the accepted container reads was not recorded: %+v", got)
+	}
+	// Accepted stays accepted: the next pass with nothing moved is quiet too.
+	m.asked = nil
+	report, known = applyCarried(t, d, known, m, nil)
+	if m.did("docker rm") || m.did("docker run") || report.Changed() {
+		t.Fatalf("an accepted container was recreated on the pass after: %v", m.asked)
+	}
+
+	// And a change to the file is caught from the record, and the label is renewed.
+	m.asked = nil
+	report, _ = applyCarried(t, declare("5433"), known, m, nil)
+	if !m.removed("forge") || !m.did("docker run") {
+		t.Fatalf("an accepted container was not recreated when its env-file changed: %v", m.asked)
+	}
+	if o := outcomeOf(report, "forge.server"); o.Detail != "recreated: "+env+" changed" {
+		t.Errorf("the recreate did not name the file: %+v", o)
+	}
+	if m.containers["forge"].spec == legacy {
+		t.Error("the recreated container still carries the legacy label")
+	}
+}
+
+func TestAContainerAdoptedUnderANewIdStillSaysWhichFileChanged(t *testing.T) {
+	// The bundle's `store` becomes the postgres module's `postgres.server`: the same container by
+	// name, under a new id with no record of its own. A file change on that day is a real change,
+	// and the record of what it read is under the old id — by name, it is found.
+	dir := t.TempDir()
+	env := filepath.Join(dir, "store.env")
+	m := &machine{containers: map[string]*fakeContainer{}}
+	raised := parseTrusted(t, `{"declaration":1,"resources":[
+	  {"id":"env","type":"file","path":"`+env+`","content":"PORT=5432\n","mode":"0600"},
+	  {"id":"store","type":"container","name":"mesh-store","image":"`+pinned+`","env-file":["`+env+`"]}
+	]}`)
+	_, known := applyCarried(t, raised, store.State{}, m, nil)
+
+	adopted := parseTrusted(t, `{"declaration":1,"resources":[
+	  {"id":"postgres.env","type":"file","path":"`+env+`","content":"PORT=5433\n","mode":"0600"},
+	  {"id":"postgres.server","type":"container","name":"mesh-store","image":"`+pinned+`","env-file":["`+env+`"]}
+	]}`)
+	m.asked = nil
+	report, _, err := Apply(context.Background(), archHost(t), adopted, known, store.OriginDeclared, m.run, nil, nil)
+	if err != nil {
+		t.Fatal(err)
+	}
+	if o := outcomeOf(report, "postgres.server"); o.Action != "updated" || o.Detail != "recreated: "+env+" changed" {
+		t.Errorf("a container adopted under a new id did not say which file changed: %+v", o)
+	}
+}
+
+func TestAHeldContainerIsNotRecreatedByAChangedHeldFile(t *testing.T) {
+	// On an adopted node the predecessor's container and the file it reads are both held as
+	// found (novox/hq ADR 0100). The predecessor rewriting its own file is reported on the file
+	// — and is nothing to recreate the container for: it is not the host's to recreate.
+	dir := t.TempDir()
+	env := filepath.Join(dir, "hello.env")
+	if err := os.WriteFile(env, []byte("PORT=5432\n"), 0o600); err != nil {
+		t.Fatal(err)
+	}
+	m := &machine{containers: map[string]*fakeContainer{
+		"hello-web": {id: "predecessor-id", running: true},
+	}}
+	d := adopted(t, untaken("hello-web.env", "hello-web.server"),
+		`{"id":"hello-web.env","type":"file","path":"`+env+`","content":"PORT=5433\n","mode":"0600"},
+		 {"id":"hello-web.server","type":"container","name":"hello-web","image":"`+pinned+`","env-file":["`+env+`"]}`)
+	report, state := applyAdopted(t, d, store.State{}, m, dir)
+	if outcomeOf(report, "hello-web.env").Action != "held" || outcomeOf(report, "hello-web.server").Action != "held" {
+		t.Fatalf("the predecessor's file and container were not held: %+v", report.Outcomes)
+	}
+
+	if err := os.WriteFile(env, []byte("PORT=5434\n"), 0o600); err != nil {
+		t.Fatal(err)
+	}
+	m.asked = nil
+	report, state = applyAdopted(t, d, state, m, dir)
+	for _, a := range m.asked {
+		if strings.HasPrefix(a, "docker run") || strings.HasPrefix(a, "docker rm") {
+			t.Fatalf("a held container was acted on because a held file changed: %s", a)
+		}
+	}
+	if o := outcomeOf(report, "hello-web.server"); o.Action != "held" {
+		t.Errorf("the container is no longer held: %+v", o)
+	}
+	if h, _ := state.HeldAt("hello-web.env"); h.Changed != "rewritten" {
+		t.Errorf("the predecessor's rewrite was not reported on the file: %+v", h)
+	}
+	if h, _ := state.HeldAt("hello-web.server"); h.Changed != "" {
+		t.Errorf("a file change was charged to the container: %+v", h)
+	}
+}

internal/apply/runonce_test.go

@@ -69,7 +69,7 @@ func TestARunOnceStepIsRunToCompletionNotLeftRunning(t *testing.T) {
 	if !ok {
 		t.Fatal("a completed run-once step was not recorded")
 	}
-	if applied.Wrote != containerSpec(d.Resources[0].(*declaration.Container), nil) {
+	if applied.Wrote != containerSpec(d.Resources[0].(*declaration.Container), inputs{}) {
 		t.Errorf("the run-once record is not the declaration's digest: %q", applied.Wrote)
 	}
 }
@@ -155,7 +155,7 @@ func TestARunOnceStepAlreadyCompletedIsNotReRun(t *testing.T) {
 	d := parseTrusted(t, `{"declaration":1,"resources":[
 	  {"id":"seed","type":"container","name":"seed","image":"`+pinned+`","run-once":true}
 	]}`)
-	want := containerSpec(d.Resources[0].(*declaration.Container), nil)
+	want := containerSpec(d.Resources[0].(*declaration.Container), inputs{})
 
 	var ran bool
 	run := func(ctx context.Context, name string, args ...string) (string, error) {
@@ -232,7 +232,7 @@ func TestARunOnceStepRunsAgainWhenWhatItReadsChanged(t *testing.T) {
 	was := map[string]string{"env": declaredDigest(&declaration.File{Content: "ACME_ROOTS=https://10.0.0.1/roots.pem\n"})}
 	known := store.State{}
 	known.Record(store.Applied{ID: "trust", Type: "container", Origin: store.OriginCarried, Target: "trust",
-		Wrote: containerSpec(d.Resources[1].(*declaration.Container), was)})
+		Wrote: containerSpec(d.Resources[1].(*declaration.Container), inputs{declares: was})})
 
 	var ran bool
 	run := func(ctx context.Context, name string, args ...string) (string, error) {
@@ -262,7 +262,7 @@ func TestARunOnceStepRunsAgainWhenWhatItReadsChanged(t *testing.T) {
 	settled := store.State{}
 	settled.Record(store.Applied{ID: "env", Type: "file", Origin: store.OriginCarried, Target: env, Wrote: now["env"]})
 	settled.Record(store.Applied{ID: "trust", Type: "container", Origin: store.OriginCarried, Target: "trust",
-		Wrote: containerSpec(d.Resources[1].(*declaration.Container), now)})
+		Wrote: containerSpec(d.Resources[1].(*declaration.Container), inputs{declares: now})})
 	if _, _, err := Apply(context.Background(), archHost(t), d, settled, store.OriginCarried, run, nil, nil); err != nil {
 		t.Fatalf("re-apply failed: %v", err)
 	}
@@ -280,7 +280,7 @@ func TestAContainerNamingARunOnceStepIsRecreatedWhenItRan(t *testing.T) {
 	  {"id":"server","type":"container","name":"server","image":"`+pinned+`","restart-on":["trust"]}
 	]}`)
 	declares := map[string]string{"trust": declaredDigest(d.Resources[0].(*declaration.Container))}
-	spec := containerSpec(d.Resources[1].(*declaration.Container), declares)
+	spec := containerSpec(d.Resources[1].(*declaration.Container), inputs{declares: declares})
 
 	var removed, created bool
 	run := func(ctx context.Context, name string, args ...string) (string, error) {

internal/apply/schedule.go

@@ -122,7 +122,7 @@ func (s *Scheduler) Sync(d *declaration.Declaration, held map[string]bool) {
 		// Nothing to read: a scheduled container may not declare restart-on — it runs to completion
 		// on its cadence rather than staying running to be restarted — so its identity cannot
 		// depend on another resource's content and there is nothing to pass.
-		spec := containerSpec(c, nil)
+		spec := containerSpec(c, inputs{})
 		if existing := s.jobs[c.Identity()]; existing != nil && existing.spec == spec {
 			// Unchanged: keep where it is in its cadence, refresh the declaration pointer only.
 			existing.container = c

internal/bootstrap/adopt_in_place_test.go

@@ -0,0 +1,130 @@
+package bootstrap
+
+import (
+	"context"
+	"errors"
+	"os"
+	"path/filepath"
+	"strings"
+	"testing"
+
+	"github.com/novox/mesh-host/internal/apply"
+	"github.com/novox/mesh-host/internal/declaration"
+	"github.com/novox/mesh-host/internal/store"
+)
+
+// Defends phase three's premise (phase3.go): the store genesis raised is adopted by the postgres
+// module IN PLACE — same name, same image, same spec — so the applier reconciles it and never
+// recreates the mesh's memory with the temporary control plane connected to it.
+//
+// The host folds a mounted file's content into the container's spec (novox/hq 04-ISSUES/103), so
+// this now depends on a byte: the superuser file genesis writes and mounts must be the same bytes
+// the module later declares. The module's value is what `secret accept` took — the operator's
+// file with its line ending removed and nothing else (mesh-control, asSupplied). Reproduced before
+// it was fixed: genesis wrote `value\n`, the module wrote `value`, and the store was recreated
+// during install.
+
+// labelled is a runtime that keeps the spec label the host gives a container and hands it back.
+type labelled struct {
+	spec    map[string]string
+	created []string
+	removed []string
+}
+
+func (l *labelled) run(_ context.Context, _ string, args ...string) (string, error) {
+	switch args[0] {
+	case "info":
+		return "27.0\n", nil
+	case "inspect":
+		spec, ok := l.spec[args[len(args)-1]]
+		if !ok {
+			return "", errors.New("no such container")
+		}
+		return "true\t" + spec + "\n", nil
+	case "rm":
+		l.removed = append(l.removed, args[len(args)-1])
+		delete(l.spec, args[len(args)-1])
+	case "run":
+		var name, spec string
+		for i, a := range args {
+			if a == "--name" {
+				name = args[i+1]
+			}
+			if a == "--label" && strings.HasPrefix(args[i+1], "mesh-host.spec=") {
+				spec = strings.TrimPrefix(args[i+1], "mesh-host.spec=")
+			}
+		}
+		l.spec[name] = spec
+		l.created = append(l.created, name)
+		return "made\n", nil
+	}
+	return "", nil
+}
+
+func TestTheStoreGenesisRaisedIsAdoptedInPlaceNotRecreated(t *testing.T) {
+	dir := t.TempDir()
+	secret := filepath.Join(dir, "superuser.secret")
+
+	// The bytes genesis really writes — the code path, not a fixture that agrees with it.
+	if _, made, err := keptOrMade(secret, false); err != nil || !made {
+		t.Fatalf("genesis did not make the superuser secret: made=%v err=%v", made, err)
+	}
+	onDisk, err := os.ReadFile(secret)
+	if err != nil {
+		t.Fatal(err)
+	}
+
+	image := "docker.io/library/postgres@sha256:" + strings.Repeat("ab", 32)
+	mounts := `"volumes":["mesh-store-data:/var/lib/postgresql/data","` + secret + `:` + storeSuperuserMount + `:ro"]`
+
+	// The foundation's store, as the produced bundle raises it (RewriteRoot): the file mounted,
+	// declared by nothing — genesis wrote it before there was a declaration to name it.
+	raise, err := declaration.ParseTrusted([]byte(`{"declaration":1,"resources":[
+	  {"id":"` + StoreID + `","type":"container","name":"mesh-store","image":"` + image + `",
+	   "env":{"POSTGRES_PASSWORD_FILE":"` + storeSuperuserMount + `"},` + mounts + `}
+	]}`))
+	if err != nil {
+		t.Fatal(err)
+	}
+	runtime := &labelled{spec: map[string]string{}}
+	_, known, err := apply.Apply(context.Background(), arch(t), raise, store.State{}, store.OriginCarried,
+		runtime.run, nil, nil)
+	if err != nil {
+		t.Fatalf("raising the foundation's store: %v", err)
+	}
+	if len(runtime.created) != 1 {
+		t.Fatalf("the store was not raised once: %v", runtime.created)
+	}
+
+	// The postgres module's declaration of the same store: the superuser file as `secret accept`
+	// took it in — its line ending removed and nothing else — then the same container.
+	accepted := strings.TrimRight(string(onDisk), "\r\n")
+	adopt, err := declaration.ParseTrusted([]byte(`{"declaration":1,"resources":[
+	  {"id":"postgres.superuser","type":"file","path":"` + secret + `","content":"` + accepted + `","mode":"0600"},
+	  {"id":"postgres.server","type":"container","name":"mesh-store","image":"` + image + `",
+	   "env":{"POSTGRES_PASSWORD_FILE":"` + storeSuperuserMount + `"},` + mounts + `}
+	]}`))
+	if err != nil {
+		t.Fatal(err)
+	}
+	runtime.created, runtime.removed = nil, nil
+	report, _, err := apply.Apply(context.Background(), arch(t), adopt, known, store.OriginDeclared,
+		runtime.run, nil, nil)
+	if err != nil {
+		t.Fatalf("adopting the store: %v", err)
+	}
+
+	if len(runtime.removed) > 0 || len(runtime.created) > 0 {
+		t.Fatalf("the module's declaration recreated the store genesis raised (removed %v, created %v): "+
+			"the file genesis mounted and the file the module declares are not the same bytes",
+			runtime.removed, runtime.created)
+	}
+	for _, o := range report.Outcomes {
+		if o.ID == "postgres.server" && o.Action != "unchanged" {
+			t.Errorf("the store was not adopted in place: %+v", o)
+		}
+		if o.ID == "postgres.superuser" && o.Action != "unchanged" {
+			t.Errorf("the module rewrote the superuser file genesis wrote: %+v", o)
+		}
+	}
+}

internal/bootstrap/rootsecrets.go

@@ -102,8 +102,16 @@ func keptOrMade(path string, dryRun bool) (value string, made bool, err error) {
 	}
 	// Written whole and renamed into place, at 0600, owned by whoever runs the installer — root,
 	// which is also who the host runs as when it later writes the sealed copy here.
+	//
+	// **The value alone, no line ending.** The module that adopts the store declares this same
+	// file, and what it declares is the value as `secret accept` took it — its line ending gone,
+	// by design. The host folds a mounted file's content into the container's spec (novox/hq
+	// 04-ISSUES/103), so a genesis that wrote `value\n` here would raise a store whose label
+	// digests one byte more than the module's file, and phase three would RECREATE the store it
+	// meant to adopt in place, with the temporary control plane connected to it. readCredentialFile
+	// tolerates either ending, so a file an earlier genesis wrote still reads.
 	tmp := path + ".genesis"
-	if err := os.WriteFile(tmp, []byte(value+"\n"), 0o600); err != nil {
+	if err := os.WriteFile(tmp, []byte(value), 0o600); err != nil {
 		return "", false, err
 	}
 	if err := os.Rename(tmp, path); err != nil {

internal/declaration/declaration.go

@@ -782,12 +782,17 @@ type Container struct {
 	// RestartOn names resources whose change means this container must be recreated — the same
 	// field a service has, for the same reason (novox/hq 04-ISSUES/009). A container reads a
 	// mounted file once at start; a changed file leaves the running process holding the old value,
-	// while every check passes because the file on disk is right. The container's spec — image,
-	// env, volumes — does not include a mounted file's *content*, so a settings change that
-	// re-renders that file is invisible to the ordinary spec diff. This closes that: the host
-	// recreates the container when one of these resources changed this pass, even if the spec
-	// matches. On a run-once step it means *run again*: a step that fetches a fact from a provider
-	// names the binding it reads, and is run again when the provider moved (novox/hq ADR 0099).
+	// while every check passes because the file on disk is right. The host recreates the container
+	// when one of these resources changed this pass, even if the spec matches.
+	//
+	// What a running container reads at creation — its env-files, and a file mounted into it
+	// directly — is part of its spec by content since novox/hq 04-ISSUES/103, and needs no naming
+	// here. A directory mounted into it is NOT looked inside, not even for files the host wrote
+	// there: whether a service reads such a file once or watches it live is the service's, and
+	// RestartOn is how a module says "once, at start" — a config the host renders under the
+	// module's state directory, a step whose result it consumes. On a run-once step it means *run
+	// again*: a step that fetches a fact from a provider names the binding it reads, and is run
+	// again when the provider moved (novox/hq ADR 0099).
 	RestartOn []string `json:"restart-on,omitempty"`
 
 	// RunOnce marks a container the host runs to completion rather than leaves running: a step,

internal/store/store.go

@@ -74,6 +74,14 @@ type Applied struct {
 	// each of the mesh's keys held before it set them, which of them were absent, and whether the
 	// file itself was — so undeclaring it gives the machine back exactly what it had.
 	Into *Into `json:"into,omitempty"`
+
+	// Reads is, for a container, the digest of each file it was created reading — its env-files
+	// and the files mounted into it — by path (novox/hq 04-ISSUES/103).
+	//
+	// A container takes those in once, when it is created, and the digest of the whole is in the
+	// container's spec label; this is the same information kept per file, so that when the spec
+	// no longer matches the host can say WHICH file changed rather than only that something did.
+	Reads map[string]string `json:"reads,omitempty"`
 }
 
 // Into is what a file written into held before the mesh's keys.
@@ -172,6 +180,28 @@ func (s State) Recorded(kind, target string) bool {
 	return false
 }
 
+// At returns what this host has a record of putting at a target of this kind, under any id and of
+// any origin — Recorded, with the record.
+//
+// By target rather than by id because the id a thing was declared under may change while the thing
+// does not: the bundle's `store` becomes a module's `postgres.server` for the same container, and
+// the file that container reads is the same file under either id. Both ids may then hold a record
+// for the one target — the bundle's is never removed by the mesh's declaration — and the most
+// recently applied is the one that says what is there now.
+func (s State) At(kind, target string) (Applied, bool) {
+	var latest Applied
+	found := false
+	for _, r := range s.Resources {
+		if r.Type != kind || r.Target != target {
+			continue
+		}
+		if !found || r.AppliedAt.After(latest.AppliedAt) {
+			latest, found = r, true
+		}
+	}
+	return latest, found
+}
+
 // HeldAt returns what is held under a resource id.
 func (s State) HeldAt(id string) (Held, bool) {
 	for _, h := range s.Held {