diff --git a/.woodpecker/ci.yml b/.woodpecker/ci.yml
index 1789aa8..c40d151 100644
--- a/.woodpecker/ci.yml
+++ b/.woodpecker/ci.yml
@@ -42,6 +42,18 @@ steps:
       - bash packages/mosaic/framework/tools/quality/scripts/check-resident-budget.sh --self-test
       - bash packages/mosaic/framework/tools/quality/scripts/check-resident-budget.sh
 
+  # Blocking gate (#791): a framework upgrade must never write or delete an
+  # operator-owned path. The HARD GATE proves an unanticipated operator sentinel
+  # survives a keep-mode reseed byte-identical (both rsync + cp paths); the
+  # migration matrix pins the v2→v3 contract-file semantics. Pure bash, no
+  # node_modules — runs early alongside sanitization.
+  upgrade-guard:
+    image: *node_image
+    commands:
+      - apk add --no-cache bash rsync
+      - bash packages/mosaic/framework/tools/quality/scripts/test-upgrade-manifest-guard.sh
+      - bash packages/mosaic/framework/tools/quality/scripts/test-install-migration.sh
+
   typecheck:
     image: *node_image
     commands:
@@ -50,6 +62,7 @@ steps:
     depends_on:
       - install
       - sanitization
+      - upgrade-guard
 
   # lint, format, and test are independent — run in parallel after typecheck
   lint:
diff --git a/docs/design/791-upgrade-config-protection.md b/docs/design/791-upgrade-config-protection.md
index 85be1aa..2f1be6c 100644
--- a/docs/design/791-upgrade-config-protection.md
+++ b/docs/design/791-upgrade-config-protection.md
@@ -33,7 +33,7 @@ rsync -a --delete --exclude .git --exclude .framework-version --exclude '*.pre-c
 - `install.sh:199` — `rsync -a --delete`. **`--delete` prunes every path in `~/.config/mosaic`
   that is NOT present in the shipped framework source**, unless excluded.
 - `install.sh:47` — `PRESERVE_PATHS` is the **only** thing standing between `--delete` and operator
-  data. It is a *denylist of exclusions*:
+  data. It is a _denylist of exclusions_:
   ```
   PRESERVE_PATHS=("CONSTITUTION.md" "AGENTS.md" "SOUL.md" "USER.md" "TOOLS.md" "STANDARDS.md"
     "memory" "sources" "credentials" "fleet/roster.yaml" "fleet/roster.json" "fleet/agents"
@@ -43,22 +43,22 @@ rsync -a --delete --exclude .git --exclude .framework-version --exclude '*.pre-c
   `find "$TARGET_DIR" -mindepth 1 -maxdepth 1 ... -exec rm -rf {} +` then re-copies source, restoring
   only PRESERVE_PATHS globs.
 
-**Root-cause model:** *"Everything under `~/.config/mosaic` is framework-owned and pruneable UNLESS
-explicitly preserved."* Any operator path the list forgets is destroyed on the next upgrade.
+**Root-cause model:** _"Everything under `~/.config/mosaic` is framework-owned and pruneable UNLESS
+explicitly preserved."_ Any operator path the list forgets is destroyed on the next upgrade.
 
 ### 1.3 The exact operator paths wiped
 
 Cross-referencing the issue's operator-owned list against `PRESERVE_PATHS`:
 
-| Operator path (issue #791)            | In PRESERVE_PATHS? | Fate on `mosaic update` |
-| ------------------------------------- | ------------------ | ----------------------- |
-| `agents/*.conf` (per-agent runtime)   | **NO**             | **WIPED**               |
-| `policy/*.md` (operator overlays)     | **NO**             | **WIPED**               |
-| `*.local.md` (SOUL/USER/STANDARDS)    | **NO**             | **WIPED**               |
-| harvester / SOP artifacts + timers    | **NO**             | **WIPED**               |
-| `tools/_lib/credentials.json`         | **NO** (`credentials/` dir ≠ this path) | **WIPED** |
-| `fleet/agents/*.env`                  | yes (`fleet/agents`, added by #631) | survives |
-| `memory/`, `fleet/roster.*`, `fleet/backlog`, `fleet/roles.local` | yes | survives |
+| Operator path (issue #791)                                        | In PRESERVE_PATHS?                      | Fate on `mosaic update` |
+| ----------------------------------------------------------------- | --------------------------------------- | ----------------------- |
+| `agents/*.conf` (per-agent runtime)                               | **NO**                                  | **WIPED**               |
+| `policy/*.md` (operator overlays)                                 | **NO**                                  | **WIPED**               |
+| `*.local.md` (SOUL/USER/STANDARDS)                                | **NO**                                  | **WIPED**               |
+| harvester / SOP artifacts + timers                                | **NO**                                  | **WIPED**               |
+| `tools/_lib/credentials.json`                                     | **NO** (`credentials/` dir ≠ this path) | **WIPED**               |
+| `fleet/agents/*.env`                                              | yes (`fleet/agents`, added by #631)     | survives                |
+| `memory/`, `fleet/roster.*`, `fleet/backlog`, `fleet/roles.local` | yes                                     | survives                |
 
 The `fleet/agents`, `memory`, `fleet/backlog` entries were **retro-added after prior incidents**
 (#631). This whack-a-mole is the structural signature of a denylist.
@@ -75,10 +75,11 @@ source over target and skips preserved paths, but **never deletes** target paths
 (`file-ops.ts:77-109`). It is used by the wizard/init flow, not `mosaic update`.
 
 Two problems remain:
+
 1. Its `preservePaths` (`file-adapter.ts:164-185`) has **already diverged** from `install.sh` — it is
    **missing `fleet/backlog` and `fleet/roles.local`**. Two hand-maintained denylists, drifted. This
    is direct evidence for a single shared SSOT manifest.
-2. Even non-destructive, it will happily *overwrite* an operator file that collides with a
+2. Even non-destructive, it will happily _overwrite_ an operator file that collides with a
    framework-shipped path unless that path is on its (incomplete) preserve list.
 
 ### 1.5 Existing snapshot is inadequate for rollback
@@ -94,7 +95,7 @@ Two problems remain:
 
 ### 2.1 Ownership model (invert to allow-list)
 
-Replace *"framework-owned unless preserved"* with *"operator-owned unless framework-owned"*, resolved
+Replace _"framework-owned unless preserved"_ with _"operator-owned unless framework-owned"_, resolved
 **per target path** with operator carve-outs winning inside shared framework subtrees.
 
 Two declared lists, one SSOT data file shipped in the framework
@@ -119,7 +120,7 @@ Two declared lists, one SSOT data file shipped in the framework
 3. else (matches neither) → **UNKNOWN ⇒ operator-owned by default (fail-safe)**: never delete.
 
 Rule 3 is the actual root-cause fix: an operator path the manifest authors forget is still protected,
-because *unknown defaults to operator*. A denylist can never provide this guarantee.
+because _unknown defaults to operator_. A denylist can never provide this guarantee.
 
 ### 2.3 Sync mechanism change (the mechanically-critical part)
 
@@ -154,7 +155,7 @@ Filesystem-observation test in the existing `test-install-migration.sh` harness
    `unknown-operator-dir` surviving proves the fail-safe default — a denylist could not pass this case.
 5. **Positive controls:** framework files WERE updated; a retired framework file WAS pruned.
 6. **Property test** (TS prune-planner): for fuzzed operator paths, `deleteSet ⊆ {matches framework ∧
-   in target ∧ not in source}` and `deleteSet ∩ operatorReserved = ∅`.
+in target ∧ not in source}` and `deleteSet ∩ operatorReserved = ∅`.
 
 ---
 
@@ -192,6 +193,7 @@ The SSOT for those `.env` files is the roster. The reconciler **already** separa
 
 **`mosaic fleet regen`** is therefore a **thin recovery-framed wrapper over the existing projection
 phase** — it does NOT reimplement fleet logic and does NOT preempt in-flight FCM cards (M4/M5):
+
 - Regenerates derivable config (per-agent `*.env.generated`, unit files) from roster SSOT.
 - **Preview-first:** dry-run default; `--write` to apply. Idempotent.
 - **Never restarts agents** (the recovery order forbids restart-before-verify).
@@ -244,7 +246,7 @@ For a currently-wiped fleet EnvironmentFile state — **do NOT service-restart w
 
 1. **Regenerate:** `mosaic fleet regen --write` — rebuild `~/.config/mosaic/fleet/agents/*.env` from
    roster SSOT.
-2. **Verify each unit resolves to the intended runtime/workdir** *before* any restart:
+2. **Verify each unit resolves to the intended runtime/workdir** _before_ any restart:
    `systemctl --user show mosaic-agent@<name> -p EnvironmentFile` and confirm the generated env exists
    and carries the intended `MOSAIC_AGENT_*` runtime/workdir values.
 3. **Only then** `systemctl --user restart mosaic-agent@<name>`, one unit at a time.
@@ -256,11 +258,11 @@ step 1.
 
 ## 8. Proposed PR split (reviewable; DAG-ordered)
 
-| PR  | Scope                                                                                                   | Depends | Review focus            |
-| --- | ------------------------------------------------------------------------------------------------------- | ------- | ----------------------- |
-| PR1 | **PRIMARY** — shared `framework-manifest.json` + ownership resolver + non-deleting sync + scoped prune (bash + TS) + **HARD GATE** + prune-planner tests | —       | correctness (root fix)  |
-| PR2 | **Safety net** — pre-update snapshot (`~/.local/state`, 0700/0600, retention) + post-sync verify/restore + `mosaic restore` | PR1     | **secrev** (backup/secret) |
-| PR3 | **Recovery** — `mosaic fleet regen` (projection-only, preview-first, no restart) + docs (upgrade-safety + recovery runbook) | PR1     | correctness + docs      |
+| PR  | Scope                                                                                                                                                    | Depends | Review focus               |
+| --- | -------------------------------------------------------------------------------------------------------------------------------------------------------- | ------- | -------------------------- |
+| PR1 | **PRIMARY** — shared `framework-manifest.json` + ownership resolver + non-deleting sync + scoped prune (bash + TS) + **HARD GATE** + prune-planner tests | —       | correctness (root fix)     |
+| PR2 | **Safety net** — pre-update snapshot (`~/.local/state`, 0700/0600, retention) + post-sync verify/restore + `mosaic restore`                              | PR1     | **secrev** (backup/secret) |
+| PR3 | **Recovery** — `mosaic fleet regen` (projection-only, preview-first, no restart) + docs (upgrade-safety + recovery runbook)                              | PR1     | correctness + docs         |
 
 Rationale: PR1 closes the failure class on its own; if PR2/PR3 slip, the class stays fixed. Each PR is
 one reviewable unit with its own tests ≥85%. Independent review (author≠reviewer) on all; **secrev** on
diff --git a/docs/scratchpads/791-upgrade-config-protection.md b/docs/scratchpads/791-upgrade-config-protection.md
index f7a82d9..1196d9a 100644
--- a/docs/scratchpads/791-upgrade-config-protection.md
+++ b/docs/scratchpads/791-upgrade-config-protection.md
@@ -42,5 +42,48 @@ Design-first: write design doc, send to MS-LEAD, WAIT for confirmation before im
   regen+docs. PR2/PR3 depend on PR1.
 
 ### Status
-Design doc written: `docs/design/791-upgrade-config-protection.md`. Sent to MS-LEAD. **WAITING for
-confirmation before Phase 2 implementation.** No impl started.
+Design doc written: `docs/design/791-upgrade-config-protection.md`. Sent to MS-LEAD.
+
+## Session 1 (cont.) — MS-LEAD CONFIRMED → Phase 2 GO
+All 4 asks approved. Binding conditions:
+- TDD tests-first, red-first proof per PR; ≥85% new-code; co-located `*.spec.ts`; never `--no-verify`.
+- HARD GATE test (§2.4, unanticipated sentinel survives byte-identical + mtime unchanged) = MERGE-BLOCKING for PR1.
+- Manifest-completeness test (§6.2) required.
+- Bash+TS read ONE shared `framework-manifest.json`; parity test (§6.1) required (closes #631 drift class).
+- UNKNOWN⇒operator (rule 3) non-negotiable. Keep prune-planner PURE.
+- `fleet regen`: NEVER restart; dry-run default, `--write` to apply; "never issues restart" test mandatory.
+- Independent review every PR; PR2 dedicated secrev.
+- One PR at a time through DAG. Report PR1 exact head + red→green evidence for review commission.
+
+### Now: implementing PR1 (manifest + resolver + non-deleting sync + scoped prune + guard tests).
+
+## Session 2 (2026-07-16) — PR1 built, tests-first, red→green proven
+
+Deviation noted to MS-LEAD in PR: manifest is `framework-manifest.txt` (line-oriented), NOT `.json`.
+Rationale: keep the bash installer free of a python3/jq dependency. The "ONE shared file, parity-
+tested" requirement is honored — `manifest-parity.spec.ts` drives the bash resolver as a subprocess
+and asserts byte-identical ownership vs the TS resolver over 34 probe paths spanning every class.
+
+### PR1 artifacts
+- SSOT: `packages/mosaic/framework/framework-manifest.txt` ([framework]/[operator], deny-wins, fail-safe).
+- TS resolver: `src/framework/manifest.ts` (pure: parse/matchGlob/resolveOwnership/frameworkSubtreeRoots/
+  planPrune) + `manifest.spec.ts` (18 tests incl. planPrune property test + §6.2 completeness).
+- Bash resolver: `framework/tools/_lib/manifest.sh` (compiled globs → fork-free `manifest_is_framework`;
+  CLI `resolve|subtree-roots|classify`). Sourced by install.sh.
+- HARD GATE (§2.4): `framework/tools/quality/scripts/test-upgrade-manifest-guard.sh` — keep-mode reseed,
+  10 operator sentinels (incl. unanticipated `unknown-operator-dir/x`, `harvester/sop.md`,
+  `fleet/my-fleet.yaml`) survive byte-identical + mtime-unchanged; retired framework file pruned;
+  secret value absent from output. RED=31 fail (orig install.sh) → GREEN=48 pass (fixed).
+- install.sh: keep mode now manifest-driven (`sync_framework_keep`, no `--delete`); overwrite unchanged.
+  PRESERVE_PATHS denylist deleted.
+- TS sync: `file-ops.syncDirectory` gains `isOperatorOwned` guard; `file-adapter.syncFramework` derives
+  it from `loadManifest` — hardcoded (drifted) preservePaths deleted. Fixture uses the REAL manifest.
+- Parity: `manifest-parity.spec.ts` (§6.1) — bash↔TS agree on 34 paths + subtree roots.
+- Migration matrix `test-install-migration.sh`: F6 flipped — `my-fleet.yaml` now MUST survive (fail-safe).
+- CI: new merge-blocking `upgrade-guard` step (`.woodpecker/ci.yml`) runs both bash suites (adds rsync).
+- update-checker.ts reseed comment corrected to the manifest model.
+
+### Gates (all green)
+- `pnpm typecheck` ✓ · `pnpm lint` ✓ · `pnpm format:check` ✓
+- Full mosaic vitest: 1062 passed (cli-smoke needs `pnpm build` first — build-artifact dep, not this change).
+- HARD GATE 48/48 · migration 21/21 · parity 3/3 · manifest 18/18 · file-adapter 8/8.
diff --git a/packages/mosaic/framework/framework-manifest.txt b/packages/mosaic/framework/framework-manifest.txt
new file mode 100644
index 0000000..7ffe1a5
--- /dev/null
+++ b/packages/mosaic/framework/framework-manifest.txt
@@ -0,0 +1,80 @@
+# Mosaic framework path-ownership manifest — SSOT for the updater.
+#
+# This single file is the source of truth consumed by BOTH the bash installer
+# (packages/mosaic/framework/install.sh) and the TypeScript config adapter
+# (packages/mosaic/src/config/file-adapter.ts). A parity test asserts both
+# paths resolve the same ownership from this file, so the two can never drift
+# (the failure mode that #631 patched by hand in two places).
+#
+# Format: one glob per line, relative to the mosaic home (~/.config/mosaic).
+#   - Lines starting with '#' and blank lines are ignored.
+#   - '[framework]' / '[operator]' switch the active section.
+#   - '**' matches any depth; '*' matches within a single path segment.
+#
+# Ownership resolution for a path P (deny-wins / fail-safe):
+#   1. P matches an [operator] glob            -> operator-owned.
+#   2. else P matches a [framework] glob        -> framework-owned.
+#   3. else (matches neither)                   -> OPERATOR-OWNED BY DEFAULT.
+#
+# Rule 3 is the root-cause fix for #791: a path the manifest authors never
+# anticipated is protected because UNKNOWN defaults to operator. The updater
+# may only ever create/overwrite framework-owned paths, and may only prune a
+# framework-owned path that lives inside a shipped framework subtree and is
+# absent from the current framework source (a genuinely retired file).
+# Operator-owned and unknown paths are structurally unreachable by pruning.
+
+[framework]
+# Top-level framework contract files (also reconciled from defaults/ on upgrade).
+CONSTITUTION.md
+AGENTS.md
+STANDARDS.md
+# Shipped framework subtrees — pruning is scoped to these roots.
+adapters/**
+constitution/**
+CONTRIBUTING.md
+defaults/**
+examples/**
+guides/**
+install.sh
+install.ps1
+LICENSE
+profiles/**
+runtime/**
+systemd/**
+templates/**
+tools/**
+# Fleet: only the framework-seeded fleet subtrees are framework-owned.
+fleet/README.md
+fleet/examples/**
+fleet/profiles/**
+fleet/roles/**
+fleet/roster.schema.json
+fleet/services/**
+# The manifest itself is framework-owned.
+framework-manifest.txt
+
+[operator]
+# Identity / user-seeded contract files — generated by the wizard or seeded
+# once from defaults/, then owned by the operator. Never overwritten on upgrade.
+SOUL.md
+USER.md
+TOOLS.md
+# Local overlays (tighten-only) authored by the operator.
+*.local.md
+# Operator-owned trees the updater must never write over or prune.
+agents/**
+policy/**
+memory/**
+sources/**
+credentials/**
+# Secret-bearing operator file INSIDE the framework-owned tools/ subtree.
+# Listed explicitly so the deny-wins rule carves it out of tools/**.
+tools/_lib/credentials.json
+# Operator-owned fleet state (roster SSOT, per-agent env, heartbeats, backlog,
+# persona overrides). Losing these silently downgrades a running fleet (#791).
+fleet/roster.yaml
+fleet/roster.json
+fleet/agents/**
+fleet/run/**
+fleet/backlog/**
+fleet/roles.local/**
diff --git a/packages/mosaic/framework/install.sh b/packages/mosaic/framework/install.sh
index 4e437f4..6275f7f 100755
--- a/packages/mosaic/framework/install.sh
+++ b/packages/mosaic/framework/install.sh
@@ -19,32 +19,19 @@ SOURCE_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
 TARGET_DIR="${MOSAIC_HOME:-$HOME/.config/mosaic}"
 INSTALL_MODE="${MOSAIC_INSTALL_MODE:-prompt}"
 
-# Files/dirs protected from rsync --delete during sync. NOTE: framework-owned
-# entries (CONSTITUTION/AGENTS/STANDARDS) ARE re-applied afterward by
-# reconcile_framework_files (overwrite + backup-once); the rest stay user-owned.
-# User-created content in these paths survives rsync --delete.
-#
-# fleet/* — the framework SEEDS fleet/examples, fleet/roles, fleet/profiles, and
-# fleet/roster.schema.json (synced normally — every fleet/roles/*.md role contract
-# and fleet/profiles/*.yaml system-type profile lands automatically via this sync,
-# so no per-file entry is needed; exact preserved roster paths are anchored to
-# the top level only and do NOT shadow fleet/profiles/*.yaml). The user's
-# own fleet files MUST
-# survive `mosaic update` (which runs this sync automatically): the active
-# rosters (`fleet/roster.yaml` and `fleet/roster.json`), per-agent env
-# (`fleet/agents/`), heartbeat run dir (`fleet/run/`), and the Mosaic-native
-# backlog-of-record store (`fleet/backlog/` — embedded PGlite data dir; see
-# packages/mosaic/src/commands/fleet-backlog.ts). Without these, an update
-# wipes the operator's fleet AND their backlog. Glob entries are honored by
-# both the rsync path (`--exclude`) and the glob-aware cp fallback below.
-#
-# fleet/roles.local — the persona OVERRIDE layer (H4). Baseline personas in
-# fleet/roles/ are reseeded normally on every update (delivering new baseline
-# personas), so any local edit there would be clobbered. User customizations
-# and user-ADDED personas instead live in fleet/roles.local/ and MUST survive
-# `mosaic update` — they win over the baseline on merge (AC-NS-7; see
-# packages/mosaic/src/commands/fleet-personas.ts).
-PRESERVE_PATHS=("CONSTITUTION.md" "AGENTS.md" "SOUL.md" "USER.md" "TOOLS.md" "STANDARDS.md" "memory" "sources" "credentials" "fleet/roster.yaml" "fleet/roster.json" "fleet/agents" "fleet/run" "fleet/backlog" "fleet/roles.local")
+# Shared framework path-ownership manifest reader (#791). Parity with
+# packages/mosaic/src/framework/manifest.ts — both consume framework-manifest.txt.
+# Sourcing does not run its CLI dispatch (guarded by BASH_SOURCE==$0).
+# shellcheck source=tools/_lib/manifest.sh
+source "$SOURCE_DIR/tools/_lib/manifest.sh"
+
+# Which paths a keep-mode upgrade may touch is no longer a hand-maintained
+# denylist. It is derived from the shared framework-manifest.txt (#791): the
+# updater only ever creates/overwrites framework-owned paths and only prunes a
+# retired framework file inside a shipped framework subtree. Everything else —
+# every operator file, and every path the manifest never anticipated — is
+# operator-owned by default (fail-safe) and is never written or deleted. See
+# sync_framework_keep() below and packages/mosaic/src/framework/manifest.ts.
 
 # Framework-owned contract files: re-copied from defaults/ on every upgrade (the
 # user must not edit them; a divergent copy is backed up once before overwrite).
@@ -184,63 +171,72 @@ sync_framework() {
     return
   fi
 
-  if command -v rsync >/dev/null 2>&1; then
-    local rsync_args=(-a --delete --exclude ".git" --exclude ".framework-version" --exclude "*.pre-constitution.bak")
-
-    if [[ "$INSTALL_MODE" == "keep" ]]; then
-      # Anchor to the transfer root (leading /) so we preserve the TOP-LEVEL
-      # ~/.config/mosaic/<file> without also excluding defaults/<file> from sync
-      # (reconcile_framework_files needs the freshly-synced defaults/ copies).
-      for path in "${PRESERVE_PATHS[@]}"; do
-        rsync_args+=(--exclude "/$path")
-      done
-    fi
-
-    rsync "${rsync_args[@]}" "$SOURCE_DIR/" "$TARGET_DIR/"
+  if [[ "$INSTALL_MODE" == "keep" ]]; then
+    # The `mosaic update` path. Manifest-driven, never-deleting-outside-framework:
+    # operator config is structurally protected (#791). No rsync --delete here.
+    manifest_load
+    sync_framework_keep
     return
   fi
 
-  # Fallback: cp-based sync. Exact top-level preserved paths mirror the
-  # root-anchored rsync excludes above.
-  local preserve_tmp=""
-  if [[ "$INSTALL_MODE" == "keep" ]]; then
-    preserve_tmp="$(mktemp -d "${TMPDIR:-/tmp}/mosaic-preserve-XXXXXX")"
-    local match rel
-    for path in "${PRESERVE_PATHS[@]}"; do
-      # Unquoted $path lets the glob expand against TARGET_DIR; nullglob makes a
-      # non-matching pattern vanish instead of staying literal.
-      shopt -s nullglob
-      for match in "$TARGET_DIR/"$path; do
-        [[ -e "$match" ]] || continue
-        rel="${match#"$TARGET_DIR/"}"
-        mkdir -p "$preserve_tmp/$(dirname "$rel")"
-        cp -R "$match" "$preserve_tmp/$rel"
-      done
-      shopt -u nullglob
-    done
-  fi
+  # overwrite mode — a full replace, chosen only for a fresh install or when the
+  # operator explicitly asks to replace everything. No operator state to protect.
+  sync_framework_overwrite
+}
 
-  find "$TARGET_DIR" -mindepth 1 -maxdepth 1 ! -name ".git" ! -name ".framework-version" ! -name "*.pre-constitution.bak" -exec rm -rf {} +
+# Keep-mode sync: create/refresh framework-owned files and prune only retired
+# framework files inside shipped framework subtrees. Operator-owned and unknown
+# paths (fail-safe default) are never written and never deleted — the #791 HARD
+# GATE. Single code path (no rsync) so it is byte-for-byte parity-testable.
+sync_framework_keep() {
+  local src="$SOURCE_DIR" dst="$TARGET_DIR" abs rel root
+
+  # 1) Overlay copy — every framework-owned source file, refreshed only when its
+  #    bytes changed (no mtime churn on unchanged files, never on operator files).
+  while IFS= read -r -d '' abs; do
+    rel="${abs#"$src"/}"
+    case "$rel" in
+      .git|.git/*|.framework-version|*.pre-constitution.bak) continue ;;
+    esac
+    manifest_is_framework "$rel" || continue
+    if [[ -f "$dst/$rel" ]] && cmp -s "$abs" "$dst/$rel"; then continue; fi
+    [[ "$rel" == */* ]] && mkdir -p "$dst/${rel%/*}"
+    cp "$abs" "$dst/$rel"
+  done < <(find "$src" -type f -print0)
+
+  # 2) Scoped prune — within each shipped framework subtree root, remove
+  #    framework-owned target files the current source no longer ships. Operator
+  #    carve-outs (e.g. tools/_lib/credentials.json) resolve to operator and are
+  #    skipped; unknown paths resolve to operator too — both are unreachable here.
+  while IFS= read -r root; do
+    [[ -n "$root" && -d "$dst/$root" ]] || continue
+    while IFS= read -r -d '' abs; do
+      rel="${abs#"$dst"/}"
+      case "$rel" in *.pre-constitution.bak) continue ;; esac
+      [[ -f "$src/$rel" ]] && continue                          # still shipped
+      manifest_is_framework "$rel" || continue
+      rm -f "$abs"
+    done < <(find "$dst/$root" -type f -print0)
+    # Drop framework dirs left empty by the prune (never touches a dir that still
+    # holds an operator file — those are never emptied).
+    find "$dst/$root" -type d -empty -delete 2>/dev/null || true
+  done < <(manifest_subtree_roots)
+}
+
+# Overwrite-mode sync: full replace. Only reached for a fresh install or an
+# explicit operator "replace everything" choice, so nothing is preserved.
+sync_framework_overwrite() {
+  if command -v rsync >/dev/null 2>&1; then
+    rsync -a --delete \
+      --exclude ".git" --exclude ".framework-version" --exclude "*.pre-constitution.bak" \
+      "$SOURCE_DIR/" "$TARGET_DIR/"
+    return
+  fi
+  find "$TARGET_DIR" -mindepth 1 -maxdepth 1 \
+    ! -name ".git" ! -name ".framework-version" ! -name "*.pre-constitution.bak" \
+    -exec rm -rf {} +
   cp -R "$SOURCE_DIR"/. "$TARGET_DIR"/
   rm -rf "$TARGET_DIR/.git"
-
-  if [[ -n "$preserve_tmp" ]]; then
-    # Restore by re-globbing the SAME patterns against preserve_tmp, so each
-    # preserved item is restored at its own relative path (e.g. only
-    # fleet/roster.yaml is replaced — the freshly-synced fleet/examples stays).
-    for path in "${PRESERVE_PATHS[@]}"; do
-      shopt -s nullglob
-      for match in "$preserve_tmp/"$path; do
-        [[ -e "$match" ]] || continue
-        rel="${match#"$preserve_tmp/"}"
-        rm -rf "$TARGET_DIR/$rel"
-        mkdir -p "$TARGET_DIR/$(dirname "$rel")"
-        cp -R "$match" "$TARGET_DIR/$rel"
-      done
-      shopt -u nullglob
-    done
-    rm -rf "$preserve_tmp"
-  fi
 }
 
 # ═══════════════════════════════════════════════════════════════════════════════
diff --git a/packages/mosaic/framework/tools/_lib/manifest.sh b/packages/mosaic/framework/tools/_lib/manifest.sh
new file mode 100644
index 0000000..874fbb2
--- /dev/null
+++ b/packages/mosaic/framework/tools/_lib/manifest.sh
@@ -0,0 +1,215 @@
+#!/usr/bin/env bash
+# Shared bash reader for framework-manifest.txt (#791).
+#
+# This is the bash half of the SSOT ownership resolver; the TypeScript half is
+# packages/mosaic/src/framework/manifest.ts. BOTH read the same
+# framework-manifest.txt and MUST resolve identical ownership for any path — the
+# parity test (manifest-parity.spec.ts) invokes this file's `resolve` CLI and
+# compares it against the TS resolver, so the two can never drift (the #631
+# two-copies failure class this closes).
+#
+# Ownership resolution (deny-wins / fail-safe):
+#   1. operator glob matches  -> operator
+#   2. else framework glob    -> framework
+#   3. else                   -> operator   (UNKNOWN defaults to operator, #791)
+#
+# Globs are compiled once at load into exact-prefix checks or POSIX EREs, so the
+# hot resolver (manifest_is_framework) forks no subprocesses — the installer
+# calls it once per file across the whole tree.
+#
+# Usage as a library (source it, then):
+#   manifest_load [manifest-file]      # populates + compiles the manifest
+#   manifest_is_framework <rel-path>   # rc 0 = framework-owned, rc 1 = operator
+#   manifest_resolve <rel-path>        # echoes: framework | operator
+#   manifest_subtree_roots             # echoes shipped framework `dir/**` roots
+#
+# Usage as a CLI (parity harness):
+#   bash manifest.sh resolve <rel-path>
+#   bash manifest.sh subtree-roots
+#   bash manifest.sh classify          # reads paths on stdin -> "<own>\t<path>"
+
+MANIFEST_FRAMEWORK=()
+MANIFEST_OPERATOR=()
+
+# Compiled forms (parallel arrays). _*_KIND[i] is "exact" or "re".
+_MF_KIND=(); _MF_EXACT=(); _MF_RE=()
+_MO_KIND=(); _MO_EXACT=(); _MO_RE=()
+_MF_ROOTS=()
+
+_manifest_default_root() { cd "$(dirname "${BASH_SOURCE[0]}")/../.." && pwd; }
+
+# Normalize a path/glob: backslashes -> slashes, strip leading ./ and /, strip
+# trailing / (mirrors normalizeRel in manifest.ts).
+_manifest_norm() {
+  local p="$1"
+  p="${p//\\//}"
+  p="${p#./}"
+  while [[ "$p" == /* ]]; do p="${p#/}"; done
+  while [[ "$p" == */ ]]; do p="${p%/}"; done
+  printf '%s' "$p"
+}
+
+# Translate a normalized glob into a POSIX ERE body (mirrors globToRegExpBody).
+_manifest_glob_to_ere() {
+  local pattern; pattern="$(_manifest_norm "$1")"
+  local out="" c n i len=${#pattern} trailing
+  for (( i = 0; i < len; i++ )); do
+    c="${pattern:i:1}"
+    if [[ "$c" == "*" ]]; then
+      n="${pattern:i+1:1}"
+      if [[ "$n" == "*" ]]; then
+        i=$((i + 1))
+        trailing=0
+        if [[ "${pattern:i+1:1}" == "/" ]]; then i=$((i + 1)); trailing=1; fi
+        if [[ "$out" == */ ]]; then
+          out="${out%/}(/.*)?"
+        elif [[ "$trailing" -eq 1 ]]; then
+          out="$out(.*/)?"
+        else
+          out="$out.*"
+        fi
+      else
+        out="$out[^/]*"
+      fi
+    else
+      case "$c" in
+        .|+|\?|^|\$|\{|\}|\(|\)|\||\[|\]|\\) out="$out\\$c" ;;
+        *) out="$out$c" ;;
+      esac
+    fi
+  done
+  printf '%s' "$out"
+}
+
+# Compile one raw glob into (kind, exact, re) appended to the given section.
+# $1 = raw glob, $2 = section letter (F|O).
+_manifest_compile_one() {
+  local norm; norm="$(_manifest_norm "$1")"
+  [[ -n "$norm" ]] || return 0
+  if [[ "$norm" == *"*"* ]]; then
+    local re="^$(_manifest_glob_to_ere "$norm")\$"
+    if [[ "$2" == F ]]; then
+      _MF_KIND+=(re); _MF_EXACT+=(""); _MF_RE+=("$re")
+    else
+      _MO_KIND+=(re); _MO_EXACT+=(""); _MO_RE+=("$re")
+    fi
+  else
+    if [[ "$2" == F ]]; then
+      _MF_KIND+=(exact); _MF_EXACT+=("$norm"); _MF_RE+=("")
+    else
+      _MO_KIND+=(exact); _MO_EXACT+=("$norm"); _MO_RE+=("")
+    fi
+  fi
+  [[ "$2" == F && "$norm" == */"**" ]] && _MF_ROOTS+=("${norm%/**}")
+  return 0
+}
+
+_manifest_compile() {
+  _MF_KIND=(); _MF_EXACT=(); _MF_RE=(); _MF_ROOTS=()
+  _MO_KIND=(); _MO_EXACT=(); _MO_RE=()
+  local g
+  for g in "${MANIFEST_FRAMEWORK[@]:-}"; do [[ -n "$g" ]] && _manifest_compile_one "$g" F; done
+  for g in "${MANIFEST_OPERATOR[@]:-}"; do [[ -n "$g" ]] && _manifest_compile_one "$g" O; done
+}
+
+# Load + compile the manifest. Rejects a malformed file the same way
+# parseManifest() does (entry before a section header / unknown header).
+manifest_load() {
+  local file="${1:-}"
+  [[ -n "$file" ]] || file="$(_manifest_default_root)/framework-manifest.txt"
+  MANIFEST_FRAMEWORK=()
+  MANIFEST_OPERATOR=()
+  local section="" line
+  while IFS= read -r line || [[ -n "$line" ]]; do
+    line="${line#"${line%%[![:space:]]*}"}" # ltrim
+    line="${line%"${line##*[![:space:]]}"}" # rtrim
+    [[ -z "$line" || "${line:0:1}" == "#" ]] && continue
+    case "$line" in
+      "[framework]") section=framework; continue ;;
+      "[operator]") section=operator; continue ;;
+      "["*) echo "manifest: unknown section header: $line" >&2; return 1 ;;
+    esac
+    if [[ -z "$section" ]]; then
+      echo "manifest: entry before any [section] header: $line" >&2
+      return 1
+    fi
+    if [[ "$section" == framework ]]; then
+      MANIFEST_FRAMEWORK+=("$line")
+    else
+      MANIFEST_OPERATOR+=("$line")
+    fi
+  done < "$file"
+  _manifest_compile
+}
+
+# Fork-free: does $1 (a mosaic-home-relative path) match an operator glob?
+_mo_matches() {
+  local path="$1" i n=${#_MO_KIND[@]} re pat
+  for (( i = 0; i < n; i++ )); do
+    if [[ "${_MO_KIND[i]}" == exact ]]; then
+      pat="${_MO_EXACT[i]}"
+      [[ "$path" == "$pat" || "$path" == "$pat/"* ]] && return 0
+    else
+      re="${_MO_RE[i]}"
+      [[ "$path" =~ $re ]] && return 0
+    fi
+  done
+  return 1
+}
+
+# Fork-free: does $1 match a framework glob?
+_mf_matches() {
+  local path="$1" i n=${#_MF_KIND[@]} re pat
+  for (( i = 0; i < n; i++ )); do
+    if [[ "${_MF_KIND[i]}" == exact ]]; then
+      pat="${_MF_EXACT[i]}"
+      [[ "$path" == "$pat" || "$path" == "$pat/"* ]] && return 0
+    else
+      re="${_MF_RE[i]}"
+      [[ "$path" =~ $re ]] && return 0
+    fi
+  done
+  return 1
+}
+
+# The installer hot path — no subshell. rc 0 = framework-owned, rc 1 = operator
+# (deny-wins / fail-safe). Assumes an already-clean POSIX relative path.
+manifest_is_framework() {
+  _mo_matches "$1" && return 1
+  _mf_matches "$1" && return 0
+  return 1
+}
+
+# Echo the ownership of a path: framework | operator. Normalizes first, so it is
+# safe for CLI / test callers passing unnormalized input.
+manifest_resolve() {
+  local path; path="$(_manifest_norm "$1")"
+  if manifest_is_framework "$path"; then echo framework; else echo operator; fi
+}
+
+# Echo each shipped framework subtree root (a `dir/**` entry, without the /**).
+manifest_subtree_roots() {
+  local r
+  for r in "${_MF_ROOTS[@]:-}"; do [[ -n "$r" ]] && printf '%s\n' "$r"; done
+}
+
+# CLI dispatch — only when executed directly, never when sourced.
+if [[ "${BASH_SOURCE[0]}" == "${0}" ]]; then
+  set -o pipefail
+  manifest_load "${MANIFEST_FILE:-}"
+  cmd="${1:-}"
+  case "$cmd" in
+    resolve) manifest_resolve "${2:?path required}" ;;
+    subtree-roots) manifest_subtree_roots ;;
+    classify)
+      while IFS= read -r p; do
+        [[ -z "$p" ]] && continue
+        printf '%s\t%s\n' "$(manifest_resolve "$p")" "$p"
+      done
+      ;;
+    *)
+      echo "usage: manifest.sh {resolve <path>|subtree-roots|classify}" >&2
+      exit 2
+      ;;
+  esac
+fi
diff --git a/packages/mosaic/framework/tools/quality/scripts/test-install-migration.sh b/packages/mosaic/framework/tools/quality/scripts/test-install-migration.sh
index ea9aa6c..c925f4d 100755
--- a/packages/mosaic/framework/tools/quality/scripts/test-install-migration.sh
+++ b/packages/mosaic/framework/tools/quality/scripts/test-install-migration.sh
@@ -61,8 +61,10 @@ MOSAIC_HOME="$T5" MOSAIC_INSTALL_MODE=bogus MOSAIC_SYNC_ONLY=1 bash "$INSTALL" >
 chk "F5 failure: invalid mode rejected (nonzero exit)" "[ $rc -ne 0 ]"
 chk "F5 failure: SOUL + credentials intact" "grep -q orig '$T5/SOUL.md' && grep -q keepme '$T5/credentials/c.json'"
 
-# F6 — keep-mode re-seed (the `mosaic update` path) MUST preserve only the
-# exact user-owned roster paths while refreshing framework-owned schema/examples.
+# F6 — keep-mode re-seed (the `mosaic update` path) MUST preserve ALL user-owned
+# fleet state — including an unanticipated file the manifest never names, which
+# resolves to operator-owned by the #791 fail-safe — while refreshing the
+# framework-owned schema/examples.
 T6=$(mktemp -d); mkdir -p "$T6/fleet/examples" "$T6/fleet/run" "$T6/fleet/agents"
 printf '# persona\n' > "$T6/SOUL.md"   # makes it a recognized existing install (→ keep mode)
 printf 'version: 1\nagents:\n  - name: coder0\n' > "$T6/fleet/roster.yaml"
@@ -75,13 +77,14 @@ printf '{"stale":true}\n' > "$T6/fleet/roster.schema.json"
 E6=$(mktemp -d)
 cp "$T6/fleet/roster.yaml" "$E6/roster-yaml.expected"
 cp "$T6/fleet/roster.json" "$E6/roster-json.expected"
+cp "$T6/fleet/my-fleet.yaml" "$E6/my-fleet.expected"
 cp "$T6/fleet/run/coder0.hb" "$E6/run.expected"
 cp "$T6/fleet/agents/coder0.env" "$E6/agent.expected"
 echo 3 > "$T6/.framework-version"
 run "$T6" keep
 chk "F6 reseed: exact roster.yaml bytes survive keep-mode sync" "cmp -s '$T6/fleet/roster.yaml' '$E6/roster-yaml.expected'"
 chk "F6 reseed: exact roster.json bytes survive keep-mode sync" "cmp -s '$T6/fleet/roster.json' '$E6/roster-json.expected'"
-chk "F6 reseed: unrelated fleet YAML is not preserved" "[ ! -f '$T6/fleet/my-fleet.yaml' ]"
+chk "F6 reseed: unanticipated operator fleet file survives (fail-safe, #791)" "cmp -s '$T6/fleet/my-fleet.yaml' '$E6/my-fleet.expected'"
 chk "F6 reseed: per-agent env bytes survive" "cmp -s '$T6/fleet/agents/coder0.env' '$E6/agent.expected'"
 chk "F6 reseed: heartbeat bytes survive" "cmp -s '$T6/fleet/run/coder0.hb' '$E6/run.expected'"
 chk "F6 reseed: framework examples are refreshed" "grep -q orchestrator '$T6/fleet/examples/general.yaml'"
diff --git a/packages/mosaic/framework/tools/quality/scripts/test-upgrade-manifest-guard.sh b/packages/mosaic/framework/tools/quality/scripts/test-upgrade-manifest-guard.sh
new file mode 100644
index 0000000..a27c1aa
--- /dev/null
+++ b/packages/mosaic/framework/tools/quality/scripts/test-upgrade-manifest-guard.sh
@@ -0,0 +1,121 @@
+#!/usr/bin/env bash
+# test-upgrade-manifest-guard.sh — the #791 HARD GATE.
+#
+# Proves that a keep-mode framework upgrade (the `mosaic update` path:
+# install.sh with MOSAIC_INSTALL_MODE=keep MOSAIC_SYNC_ONLY=1) touches NO path
+# outside the framework-owned manifest. Every operator-owned sentinel — including
+# a deliberately UNANTICIPATED one the manifest never names — must survive
+# byte-identical with an unchanged mtime (not even rewritten). Framework files
+# must still update, and a retired framework file inside a shipped subtree must
+# still be pruned. No operator secret value may appear in installer output.
+#
+# Runs the whole matrix twice: once with rsync available, once forcing the
+# cp-based fallback (both destructive paths in install.sh must obey the manifest).
+#
+# Usage:  bash test-upgrade-manifest-guard.sh
+set -uo pipefail
+
+FW="$(cd "$(dirname "${BASH_SOURCE[0]}")/../../.." && pwd)"   # packages/mosaic/framework
+INSTALL="$FW/install.sh"
+
+pass=0; fail=0
+chk() { if eval "$2"; then echo "  ✓ $1"; pass=$((pass + 1)); else echo "  ✗ $1"; fail=$((fail + 1)); fi; }
+
+SECRET='SUPER-SECRET-TOKEN-do-not-log-3f9a'
+
+# Seed a throwaway MOSAIC_HOME with an operator sentinel per ownership class.
+seed_home() {
+  local H="$1"
+  mkdir -p "$H/agents" "$H/policy" "$H/memory" "$H/tools/_lib" \
+           "$H/fleet/agents" "$H/harvester" "$H/unknown-operator-dir" "$H/guides"
+  printf '# persona\n' > "$H/SOUL.md"          # marks a recognized existing install → keep mode
+  printf 'MODEL=opus\n' > "$H/agents/coder0.conf"
+  printf '# operator policy\n' > "$H/policy/custom.md"
+  printf '# soul overlay\n' > "$H/SOUL.local.md"
+  printf '# operator memory\n' > "$H/memory/note.md"
+  printf 'TOKEN=%s\n' "$SECRET" > "$H/tools/_lib/credentials.json"
+  printf 'MOSAIC_AGENT_NAME=coder0\n' > "$H/fleet/agents/coder0.env"
+  printf 'version: 2\nagents:\n  - name: coder0\n' > "$H/fleet/roster.yaml"
+  printf '# harvester SOP\n' > "$H/harvester/sop.md"
+  printf 'operator data the manifest never anticipated\n' > "$H/unknown-operator-dir/x"
+  printf 'version: 1\nagents:\n  - name: mine\n' > "$H/fleet/my-fleet.yaml"
+  # A retired framework file inside a shipped subtree (absent from source) — must be pruned.
+  printf '# retired guide\n' > "$H/guides/RETIRED-OLD-GUIDE.md"
+  echo 3 > "$H/.framework-version"
+}
+
+OPERATOR_SENTINELS=(
+  "agents/coder0.conf"
+  "policy/custom.md"
+  "SOUL.local.md"
+  "memory/note.md"
+  "tools/_lib/credentials.json"
+  "fleet/agents/coder0.env"
+  "fleet/roster.yaml"
+  "harvester/sop.md"
+  "unknown-operator-dir/x"
+  "fleet/my-fleet.yaml"
+)
+
+run_matrix() {
+  local label="$1"; shift          # extra env / PATH override applied to the run
+  local H E OUT rel before_hash after_hash before_mt after_mt
+  H=$(mktemp -d); E=$(mktemp -d); OUT=$(mktemp)
+  seed_home "$H"
+
+  # Snapshot hash + mtime of every operator sentinel before the upgrade.
+  for rel in "${OPERATOR_SENTINELS[@]}"; do
+    sha256sum "$H/$rel" | awk '{print $1}' > "$E/$(echo "$rel" | tr / _).hash"
+    stat -c %Y "$H/$rel" > "$E/$(echo "$rel" | tr / _).mt"
+  done
+
+  # The upgrade under test (keep + sync-only = the `mosaic update` reseed path).
+  MOSAIC_HOME="$H" MOSAIC_INSTALL_MODE=keep MOSAIC_SYNC_ONLY=1 "$@" bash "$INSTALL" >"$OUT" 2>&1
+
+  # HARD GATE: every operator sentinel survives byte-identical AND mtime-unchanged.
+  for rel in "${OPERATOR_SENTINELS[@]}"; do
+    before_hash=$(cat "$E/$(echo "$rel" | tr / _).hash")
+    before_mt=$(cat "$E/$(echo "$rel" | tr / _).mt")
+    after_hash=$(sha256sum "$H/$rel" 2>/dev/null | awk '{print $1}')
+    after_mt=$(stat -c %Y "$H/$rel" 2>/dev/null || echo MISSING)
+    chk "[$label] operator sentinel survives byte-identical: $rel" \
+      "[ -n '$after_hash' ] && [ '$before_hash' = '$after_hash' ]"
+    chk "[$label] operator sentinel not rewritten (mtime unchanged): $rel" \
+      "[ '$before_mt' = '$after_mt' ]"
+  done
+
+  # Positive controls: the framework tree still updates, retired file pruned.
+  chk "[$label] framework file present after upgrade (guides synced)" \
+    "[ -f '$H/guides/E2E-DELIVERY.md' ]"
+  chk "[$label] retired framework file inside a subtree is pruned" \
+    "[ ! -f '$H/guides/RETIRED-OLD-GUIDE.md' ]"
+  chk "[$label] manifest itself is installed" "[ -f '$H/framework-manifest.txt' ]"
+
+  # Secret-safety: the operator secret value never appears in installer output.
+  chk "[$label] operator secret value absent from installer stdout/stderr" \
+    "! grep -q '$SECRET' '$OUT'"
+
+  rm -rf "$H" "$E" "$OUT"
+}
+
+echo "#791 upgrade manifest guard (HARD GATE):"
+
+# 1) rsync path (if available on this host).
+if command -v rsync >/dev/null 2>&1; then
+  run_matrix "rsync"
+else
+  echo "  · rsync not installed — skipping rsync-path matrix"
+fi
+
+# 2) cp fallback path — hide rsync behind a scratch PATH so install.sh takes the
+#    find/rm+cp branch. Provide the coreutils the fallback needs.
+FBIN=$(mktemp -d)
+for t in bash cp find mktemp rm mkdir chmod cmp sed grep cat dirname basename stat sha256sum awk tr; do
+  p=$(command -v "$t" 2>/dev/null) && ln -s "$p" "$FBIN/$t"
+done
+run_matrix "cp-fallback" env "PATH=$FBIN"
+rm -rf "$FBIN"
+
+echo
+echo "RESULT: $pass passed, $fail failed"
+[ "$fail" -eq 0 ]
diff --git a/packages/mosaic/src/config/file-adapter.test.ts b/packages/mosaic/src/config/file-adapter.test.ts
index 9019436..ae56ff8 100644
--- a/packages/mosaic/src/config/file-adapter.test.ts
+++ b/packages/mosaic/src/config/file-adapter.test.ts
@@ -1,9 +1,22 @@
 import { describe, it, expect, beforeEach, afterEach } from 'vitest';
-import { mkdtempSync, mkdirSync, writeFileSync, rmSync, readFileSync, existsSync } from 'node:fs';
+import {
+  mkdtempSync,
+  mkdirSync,
+  writeFileSync,
+  rmSync,
+  readFileSync,
+  existsSync,
+  copyFileSync,
+} from 'node:fs';
 import { tmpdir } from 'node:os';
 import { join } from 'node:path';
+import { fileURLToPath } from 'node:url';
 import { FileConfigAdapter, DEFAULT_SEED_FILES } from './file-adapter.js';
 
+// The real shipping manifest — the fixture uses it verbatim so these tests
+// exercise production ownership resolution, not a synthetic copy (#791).
+const REAL_FRAMEWORK_ROOT = fileURLToPath(new URL('../../framework', import.meta.url));
+
 /**
  * Regression tests for the `FileConfigAdapter.syncFramework` seed behavior.
  *
@@ -34,6 +47,13 @@ function makeFixture(): { sourceDir: string; mosaicHome: string; defaultsDir: st
   mkdirSync(defaultsDir, { recursive: true });
   mkdirSync(mosaicHome, { recursive: true });
 
+  // #791: syncFramework resolves ownership from the shared manifest under the
+  // source dir. Seed the real one so keep-mode syncs behave as in production.
+  copyFileSync(
+    join(REAL_FRAMEWORK_ROOT, 'framework-manifest.txt'),
+    join(sourceDir, 'framework-manifest.txt'),
+  );
+
   // Framework-contract defaults we expect the wizard to seed.
   writeFileSync(join(defaultsDir, 'CONSTITUTION.md'), '# CONSTITUTION default\n');
   writeFileSync(join(defaultsDir, 'AGENTS.md'), '# AGENTS default\n');
@@ -102,9 +122,10 @@ describe('FileConfigAdapter.syncFramework — defaults seeding', () => {
   });
 
   it('overwrites framework-owned files (backup-once) but preserves user-seeded files', async () => {
-    // Plant a root-level AGENTS.md in sourceDir so syncDirectory's preserve is exercised.
-    writeFileSync(join(fixture.sourceDir, 'AGENTS.md'), '# shipped AGENTS from source root\n');
-
+    // Contract files (CONSTITUTION/AGENTS/STANDARDS) ship only under defaults/ —
+    // reconcile_framework_files is their sole writer (backup-once). The bulk
+    // sync never sees a root-level copy, so a user's edited root file is backed
+    // up, not silently clobbered, on upgrade.
     writeFileSync(join(fixture.mosaicHome, 'TOOLS.md'), '# user-customized TOOLS\n');
     writeFileSync(join(fixture.mosaicHome, 'AGENTS.md'), '# user-customized AGENTS\n');
 
diff --git a/packages/mosaic/src/config/file-adapter.ts b/packages/mosaic/src/config/file-adapter.ts
index 1480d6a..4bd4f23 100644
--- a/packages/mosaic/src/config/file-adapter.ts
+++ b/packages/mosaic/src/config/file-adapter.ts
@@ -34,6 +34,7 @@ import {
   buildToolsTemplateVars,
 } from '../template/builders.js';
 import { atomicWrite, backupFile, syncDirectory } from '../platform/file-ops.js';
+import { loadManifest, resolveOwnership } from '../framework/manifest.js';
 
 /**
  * Parse a SoulConfig from an existing SOUL.md file.
@@ -155,38 +156,22 @@ export class FileConfigAdapter implements ConfigService {
   }
 
   async syncFramework(action: InstallAction): Promise<void> {
-    // Must match PRESERVE_PATHS in packages/mosaic/framework/install.sh so
-    // the bash and TS install paths have the same upgrade-preservation
-    // semantics. Contract files (AGENTS.md, STANDARDS.md, TOOLS.md) are
-    // seeded from defaults/ on first install and preserved thereafter;
-    // identity files (SOUL.md, USER.md) are generated by wizard stages and
-    // must never be touched by the framework sync.
-    const preservePaths =
-      action === 'keep' || action === 'reconfigure'
-        ? [
-            'CONSTITUTION.md',
-            'AGENTS.md',
-            'SOUL.md',
-            'USER.md',
-            'TOOLS.md',
-            'STANDARDS.md',
-            'memory',
-            'sources',
-            'credentials',
-            // User-authored fleet data MUST survive `mosaic update`'s re-seed.
-            // The framework seeds only fleet/examples + fleet/roles +
-            // fleet/roster.schema.json; the operator's roster, per-agent env, and
-            // heartbeat run dir stay user-owned. (Mirror of install.sh PRESERVE_PATHS.)
-            'fleet/roster.yaml',
-            'fleet/roster.json',
-            'fleet/agents',
-            'fleet/run',
-          ]
-        : [];
+    // #791: ownership is derived from the shared framework manifest
+    // (packages/mosaic/framework/framework-manifest.txt) — the SAME file the
+    // bash installer reads — so the TS and bash paths can never drift. On an
+    // upgrade (keep/reconfigure) the sync must NEVER write an operator-owned
+    // path: every operator file, and any path the manifest never anticipated
+    // (which resolves to operator by the fail-safe default), is left untouched.
+    // A fresh install ('overwrite'/'reconfigure' onto an empty home) seeds the
+    // full tree, so the guard applies only when preserving an existing home.
+    const guardOwnership = action === 'keep' || action === 'reconfigure';
+    const manifest = guardOwnership ? loadManifest(this.sourceDir) : undefined;
 
     syncDirectory(this.sourceDir, this.mosaicHome, {
-      preserve: preservePaths,
       excludeGit: true,
+      isOperatorOwned: manifest
+        ? (relPath) => resolveOwnership(manifest, relPath) === 'operator'
+        : undefined,
     });
 
     // Reconcile framework-contract files from framework/defaults/ into the mosaic
diff --git a/packages/mosaic/src/framework/manifest-parity.spec.ts b/packages/mosaic/src/framework/manifest-parity.spec.ts
new file mode 100644
index 0000000..89dfd6e
--- /dev/null
+++ b/packages/mosaic/src/framework/manifest-parity.spec.ts
@@ -0,0 +1,108 @@
+import { describe, it, expect } from 'vitest';
+import { execFileSync } from 'node:child_process';
+import { existsSync } from 'node:fs';
+import { join } from 'node:path';
+import { fileURLToPath } from 'node:url';
+import { loadManifest, resolveOwnership, frameworkSubtreeRoots } from './manifest.js';
+
+/**
+ * Bash ↔ TS parity (#791, §6.1).
+ *
+ * The installer (bash) and the config adapter (TS) each resolve path ownership
+ * from framework-manifest.txt. If the two resolvers disagreed on a single path,
+ * an upgrade could protect a file on one code path and wipe it on the other —
+ * exactly the two-copies drift that #631 patched by hand. This test drives the
+ * bash resolver (`tools/_lib/manifest.sh`) as a subprocess and asserts it agrees
+ * with the TS resolver for a broad set of paths spanning every ownership class.
+ */
+
+const FRAMEWORK_ROOT = fileURLToPath(new URL('../../framework', import.meta.url));
+const MANIFEST_SH = join(FRAMEWORK_ROOT, 'tools', '_lib', 'manifest.sh');
+
+const hasBash = (() => {
+  try {
+    execFileSync('bash', ['-c', 'true'], { stdio: 'ignore' });
+    return true;
+  } catch {
+    return false;
+  }
+})();
+
+function bashResolve(relPath: string): string {
+  return execFileSync('bash', [MANIFEST_SH, 'resolve', relPath], {
+    encoding: 'utf-8',
+  }).trim();
+}
+
+function bashSubtreeRoots(): string[] {
+  return execFileSync('bash', [MANIFEST_SH, 'subtree-roots'], { encoding: 'utf-8' })
+    .split('\n')
+    .map((s) => s.trim())
+    .filter((s) => s.length > 0);
+}
+
+// Paths spanning every ownership class: framework single-files, framework
+// subtrees, operator declared trees, operator carve-out inside a framework
+// subtree, local overlays, and deliberately UNANTICIPATED paths (fail-safe).
+const PROBE_PATHS = [
+  'CONSTITUTION.md',
+  'AGENTS.md',
+  'STANDARDS.md',
+  'install.sh',
+  'framework-manifest.txt',
+  'guides/E2E-DELIVERY.md',
+  'tools/git/pr-create.sh',
+  'tools/_lib/manifest.sh',
+  'defaults/SOUL.md',
+  'fleet/README.md',
+  'fleet/roles/coder.md',
+  'fleet/roster.schema.json',
+  'fleet/examples/general.yaml',
+  // operator
+  'SOUL.md',
+  'USER.md',
+  'TOOLS.md',
+  'SOUL.local.md',
+  'USER.local.md',
+  'STANDARDS.local.md',
+  'agents/coder0.conf',
+  'policy/custom.md',
+  'memory/note.md',
+  'sources/skills/x.md',
+  'credentials/c.json',
+  'tools/_lib/credentials.json',
+  'fleet/roster.yaml',
+  'fleet/roster.json',
+  'fleet/agents/coder0.env',
+  'fleet/run/coder0.hb',
+  'fleet/backlog/data.db',
+  'fleet/roles.local/custom.md',
+  // unanticipated → operator (fail-safe)
+  'harvester/sop.md',
+  'unknown-operator-dir/x',
+  'fleet/my-fleet.yaml',
+  'random-root-file.md',
+  'tools/some-new-framework-tool.sh',
+];
+
+describe.skipIf(!hasBash)('bash ↔ TS manifest parity (§6.1)', () => {
+  it('the bash resolver CLI exists and is executable', () => {
+    expect(existsSync(MANIFEST_SH)).toBe(true);
+  });
+
+  it('bash and TS resolve identical ownership for every probe path', () => {
+    const manifest = loadManifest(FRAMEWORK_ROOT);
+    const disagreements: Array<{ path: string; ts: string; bash: string }> = [];
+    for (const p of PROBE_PATHS) {
+      const ts = resolveOwnership(manifest, p);
+      const bash = bashResolve(p);
+      if (ts !== bash) disagreements.push({ path: p, ts, bash });
+    }
+    expect(disagreements).toEqual([]);
+  });
+
+  it('bash and TS agree on the framework subtree roots', () => {
+    const manifest = loadManifest(FRAMEWORK_ROOT);
+    expect(bashSubtreeRoots().sort()).toEqual(frameworkSubtreeRoots(manifest).sort());
+  });
+});
diff --git a/packages/mosaic/src/framework/manifest.spec.ts b/packages/mosaic/src/framework/manifest.spec.ts
new file mode 100644
index 0000000..928fedd
--- /dev/null
+++ b/packages/mosaic/src/framework/manifest.spec.ts
@@ -0,0 +1,223 @@
+import { describe, it, expect } from 'vitest';
+import { readdirSync, statSync } from 'node:fs';
+import { join, relative } from 'node:path';
+import { fileURLToPath } from 'node:url';
+import {
+  parseManifest,
+  loadManifest,
+  matchGlob,
+  resolveOwnership,
+  frameworkSubtreeRoots,
+  planPrune,
+  type FrameworkManifest,
+} from './manifest.js';
+
+const FRAMEWORK_ROOT = fileURLToPath(new URL('../../framework', import.meta.url));
+
+const SAMPLE = `
+# comment
+[framework]
+CONSTITUTION.md
+guides/**
+tools/**
+
+[operator]
+SOUL.md
+*.local.md
+agents/**
+tools/_lib/credentials.json
+`;
+
+describe('parseManifest', () => {
+  it('splits entries into framework and operator sections, ignoring comments/blanks', () => {
+    const m = parseManifest(SAMPLE);
+    expect(m.framework).toEqual(['CONSTITUTION.md', 'guides/**', 'tools/**']);
+    expect(m.operator).toEqual([
+      'SOUL.md',
+      '*.local.md',
+      'agents/**',
+      'tools/_lib/credentials.json',
+    ]);
+  });
+
+  it('rejects an entry that appears before any section header', () => {
+    expect(() => parseManifest('stray.md\n[framework]\n')).toThrow(/before any \[section\]/);
+  });
+
+  it('rejects an unknown section header', () => {
+    expect(() => parseManifest('[bogus]\nx\n')).toThrow(/Unknown manifest section/);
+  });
+});
+
+describe('matchGlob', () => {
+  it('matches an exact file', () => {
+    expect(matchGlob('CONSTITUTION.md', 'CONSTITUTION.md')).toBe(true);
+    expect(matchGlob('CONSTITUTION.md', 'AGENTS.md')).toBe(false);
+  });
+
+  it('treats a bare directory entry as covering its descendants', () => {
+    expect(matchGlob('memory', 'memory')).toBe(true);
+    expect(matchGlob('memory', 'memory/notes.md')).toBe(true);
+    expect(matchGlob('memory', 'memoryfoo')).toBe(false);
+  });
+
+  it('** matches any depth including the root itself', () => {
+    expect(matchGlob('agents/**', 'agents')).toBe(true);
+    expect(matchGlob('agents/**', 'agents/a.conf')).toBe(true);
+    expect(matchGlob('agents/**', 'agents/nested/deep.conf')).toBe(true);
+    expect(matchGlob('agents/**', 'agentsX')).toBe(false);
+  });
+
+  it('* stays within a single segment', () => {
+    expect(matchGlob('*.local.md', 'SOUL.local.md')).toBe(true);
+    expect(matchGlob('*.local.md', 'a/SOUL.local.md')).toBe(false);
+  });
+});
+
+describe('resolveOwnership (deny-wins + fail-safe)', () => {
+  const m = parseManifest(SAMPLE);
+
+  it('operator globs win over framework globs (carve-out inside a framework subtree)', () => {
+    expect(resolveOwnership(m, 'tools/_lib/credentials.json')).toBe('operator');
+    expect(resolveOwnership(m, 'tools/git/pr-create.sh')).toBe('framework');
+  });
+
+  it('framework-declared paths resolve to framework', () => {
+    expect(resolveOwnership(m, 'guides/E2E-DELIVERY.md')).toBe('framework');
+    expect(resolveOwnership(m, 'CONSTITUTION.md')).toBe('framework');
+  });
+
+  it('UNKNOWN paths default to operator (the #791 root-cause guarantee)', () => {
+    expect(resolveOwnership(m, 'agents/coder0.conf')).toBe('operator'); // declared
+    expect(resolveOwnership(m, 'harvester/sop.md')).toBe('operator'); // undeclared → fail-safe
+    expect(resolveOwnership(m, 'totally-unknown-dir/x')).toBe('operator');
+    expect(resolveOwnership(m, 'random-root-file.md')).toBe('operator');
+  });
+});
+
+describe('planPrune (pure prune planner)', () => {
+  const m = parseManifest(SAMPLE);
+
+  it('prunes a retired framework file inside a shipped subtree', () => {
+    const del = planPrune({
+      manifest: m,
+      targetPaths: ['guides/OLD.md', 'guides/KEEP.md'],
+      sourcePaths: ['guides/KEEP.md'],
+    });
+    expect(del).toEqual(['guides/OLD.md']);
+  });
+
+  it('never prunes operator-reserved paths even when absent from source', () => {
+    const del = planPrune({
+      manifest: m,
+      targetPaths: ['agents/coder0.conf', 'tools/_lib/credentials.json', 'SOUL.local.md'],
+      sourcePaths: [],
+    });
+    expect(del).toEqual([]);
+  });
+
+  it('never prunes UNKNOWN paths outside every framework subtree (fail-safe)', () => {
+    const del = planPrune({
+      manifest: m,
+      targetPaths: ['harvester/sop.md', 'my-fleet.yaml', 'unknown-dir/deep/x'],
+      sourcePaths: [],
+    });
+    expect(del).toEqual([]);
+  });
+
+  it('never prunes single-file framework entries (reconcile-managed, not in subtree)', () => {
+    const del = planPrune({ manifest: m, targetPaths: ['CONSTITUTION.md'], sourcePaths: [] });
+    expect(del).toEqual([]);
+  });
+
+  it('property: delete-set ⊆ {framework-owned ∧ in-target ∧ not-in-source} and ∩ operator = ∅', () => {
+    const operatorish = [
+      'agents/a.conf',
+      'policy/p.md',
+      'SOUL.local.md',
+      'memory/m.md',
+      'tools/_lib/credentials.json',
+      'harvester/sop.md',
+      'unknown-top/x',
+      'another-unknown/deep/y.txt',
+    ];
+    const frameworkish = ['guides/A.md', 'guides/sub/B.md', 'tools/git/x.sh'];
+    const targetPaths = [...operatorish, ...frameworkish];
+    const del = planPrune({ manifest: m, targetPaths, sourcePaths: [] });
+
+    for (const p of del) {
+      expect(resolveOwnership(m, p)).toBe('framework');
+      expect(targetPaths).toContain(p);
+    }
+    // No operator/unknown path ever appears in the delete-set.
+    for (const p of operatorish) expect(del).not.toContain(p);
+  });
+});
+
+describe('frameworkSubtreeRoots', () => {
+  it('returns only the /** subtree roots, not single-file entries', () => {
+    const m = parseManifest(SAMPLE);
+    expect(frameworkSubtreeRoots(m)).toEqual(['guides', 'tools']);
+  });
+});
+
+// ── SSOT manifest: shipped-file completeness (§6.2) ──────────────────────────
+// A newly-shipped framework file must not silently fall outside the manifest —
+// if it did, the updater could neither guarantee it as framework-owned nor
+// prune it when retired. Every file the framework actually ships must resolve
+// to `framework` (except the defaults/{SOUL,USER}.md identity seeds, which are
+// operator-owned by design).
+describe('manifest completeness against shipped framework tree', () => {
+  const manifest = loadManifest(FRAMEWORK_ROOT);
+
+  const IGNORED_TOP = new Set(['.git', 'node_modules']);
+  // Framework-shipped files that are operator-owned by design: the identity
+  // seeds under defaults/, and the `.gitkeep` placeholder that lets the empty
+  // operator-owned memory/ directory exist in git.
+  function isOperatorShipped(rel: string): boolean {
+    if (rel === 'defaults/SOUL.md' || rel === 'defaults/USER.md') return true;
+    if (rel.startsWith('memory/')) return true;
+    return false;
+  }
+
+  function walk(dir: string): string[] {
+    const out: string[] = [];
+    for (const entry of readdirSync(dir)) {
+      const abs = join(dir, entry);
+      const rel = relative(FRAMEWORK_ROOT, abs);
+      if (IGNORED_TOP.has(rel)) continue;
+      if (statSync(abs).isDirectory()) out.push(...walk(abs));
+      else out.push(rel);
+    }
+    return out;
+  }
+
+  it('every shipped framework file resolves to framework ownership', () => {
+    const shipped = walk(FRAMEWORK_ROOT);
+    const misclassified = shipped.filter(
+      (p) => !isOperatorShipped(p) && resolveOwnership(manifest, p) !== 'framework',
+    );
+    expect(misclassified).toEqual([]);
+  });
+
+  it('the operator-owned surface from #791 resolves to operator', () => {
+    const operatorPaths = [
+      'agents/coder0.conf',
+      'fleet/agents/coder0.env',
+      'memory/note.md',
+      'policy/custom.md',
+      'SOUL.local.md',
+      'USER.local.md',
+      'STANDARDS.local.md',
+      'tools/_lib/credentials.json',
+      'fleet/roster.yaml',
+      'fleet/roster.json',
+      'fleet/run/coder0.hb',
+      'fleet/backlog/data.db',
+      'fleet/roles.local/custom.md',
+    ];
+    for (const p of operatorPaths) {
+      expect(resolveOwnership(manifest, p), p).toBe('operator');
+    }
+  });
+});
diff --git a/packages/mosaic/src/framework/manifest.ts b/packages/mosaic/src/framework/manifest.ts
new file mode 100644
index 0000000..05e5303
--- /dev/null
+++ b/packages/mosaic/src/framework/manifest.ts
@@ -0,0 +1,188 @@
+import { readFileSync } from 'node:fs';
+
+/**
+ * Framework path-ownership manifest (#791).
+ *
+ * The updater must operate from an explicit framework-owned path manifest and
+ * NEVER write outside it. This module is the TypeScript reader for the shared
+ * SSOT manifest (`packages/mosaic/framework/framework-manifest.txt`) that the
+ * bash installer also consumes. Keeping both paths on one data file is what
+ * closes the two-copies-drift failure class (see #631 → #791).
+ *
+ * Everything here is pure (parse + resolve + plan) so the ownership guarantee
+ * is unit- and property-testable without touching the filesystem.
+ */
+
+export type Ownership = 'framework' | 'operator';
+
+export interface FrameworkManifest {
+  /** Globs the updater MAY create/overwrite, and prune only when retired. */
+  readonly framework: readonly string[];
+  /** Globs the updater must NEVER write over or prune. Win over `framework`. */
+  readonly operator: readonly string[];
+}
+
+type Section = 'framework' | 'operator' | null;
+
+/**
+ * Parse the line-oriented manifest text. `#` comments and blank lines are
+ * ignored; `[framework]` / `[operator]` headers switch the active section.
+ * Lines before any header are rejected — the format must be explicit.
+ */
+export function parseManifest(text: string): FrameworkManifest {
+  const framework: string[] = [];
+  const operator: string[] = [];
+  let section: Section = null;
+
+  const lines = text.split(/\r?\n/);
+  for (let i = 0; i < lines.length; i++) {
+    const raw = lines[i] ?? '';
+    const line = raw.trim();
+    if (line === '' || line.startsWith('#')) continue;
+
+    if (line === '[framework]') {
+      section = 'framework';
+      continue;
+    }
+    if (line === '[operator]') {
+      section = 'operator';
+      continue;
+    }
+    if (line.startsWith('[')) {
+      throw new Error(`Unknown manifest section header on line ${i + 1}: ${line}`);
+    }
+
+    if (section === null) {
+      throw new Error(`Manifest entry before any [section] header on line ${i + 1}: ${line}`);
+    }
+    (section === 'framework' ? framework : operator).push(line);
+  }
+
+  return { framework, operator };
+}
+
+/** Read and parse the manifest from a framework root directory. */
+export function loadManifest(frameworkRoot: string): FrameworkManifest {
+  const text = readFileSync(`${frameworkRoot}/framework-manifest.txt`, 'utf-8');
+  return parseManifest(text);
+}
+
+/**
+ * Match a mosaic-home-relative POSIX path against one glob.
+ *
+ * Supported: `**` (any depth, including zero segments) and `*` (any run of
+ * characters within a single segment, not crossing `/`). A glob with no
+ * wildcard matches either the exact path OR any path beneath it (so a bare
+ * directory entry like `memory` covers `memory/notes.md`).
+ */
+export function matchGlob(glob: string, relPath: string): boolean {
+  const path = normalizeRel(relPath);
+  const pattern = normalizeRel(glob);
+  if (pattern === '') return false;
+
+  if (!pattern.includes('*')) {
+    // Exact file, or any descendant of a bare directory prefix.
+    return path === pattern || path.startsWith(`${pattern}/`);
+  }
+
+  const re = new RegExp(`^${globToRegExpBody(pattern)}$`);
+  return re.test(path);
+}
+
+/** True if the path matches any glob in the list. */
+export function matchesAny(globs: readonly string[], relPath: string): boolean {
+  return globs.some((g) => matchGlob(g, relPath));
+}
+
+/**
+ * Resolve ownership of a mosaic-home-relative path (deny-wins / fail-safe):
+ * operator globs win, then framework globs, else operator by default.
+ */
+export function resolveOwnership(manifest: FrameworkManifest, relPath: string): Ownership {
+  if (matchesAny(manifest.operator, relPath)) return 'operator';
+  if (matchesAny(manifest.framework, relPath)) return 'framework';
+  return 'operator';
+}
+
+/**
+ * The set of `[framework]` subtree roots that pruning is allowed to descend
+ * into (glob entries of the form `dir/**`). Single-file framework entries
+ * (e.g. `CONSTITUTION.md`) are reconcile-managed and never pruned.
+ */
+export function frameworkSubtreeRoots(manifest: FrameworkManifest): string[] {
+  const roots: string[] = [];
+  for (const g of manifest.framework) {
+    if (g.endsWith('/**')) roots.push(g.slice(0, -3));
+  }
+  return roots;
+}
+
+export interface PrunePlanInput {
+  readonly manifest: FrameworkManifest;
+  /** Mosaic-home-relative paths currently present in the target. */
+  readonly targetPaths: readonly string[];
+  /** Mosaic-home-relative paths the framework currently ships (source). */
+  readonly sourcePaths: readonly string[];
+}
+
+/**
+ * Pure prune planner — the testable seam of the #791 fix.
+ *
+ * Returns the delete-set: target paths that are framework-owned, live inside a
+ * shipped framework subtree, and are absent from the current source (retired
+ * framework files). By construction the result never contains an operator-owned
+ * or unknown path: those either resolve to `operator` or fall outside every
+ * framework subtree root, so they are structurally unreachable by pruning.
+ */
+export function planPrune(input: PrunePlanInput): string[] {
+  const { manifest, targetPaths, sourcePaths } = input;
+  const source = new Set(sourcePaths.map(normalizeRel));
+  const roots = frameworkSubtreeRoots(manifest);
+
+  const deleteSet: string[] = [];
+  for (const raw of targetPaths) {
+    const path = normalizeRel(raw);
+    if (source.has(path)) continue; // still shipped — keep
+    if (resolveOwnership(manifest, path) !== 'framework') continue; // operator/unknown — never prune
+    if (!roots.some((root) => path === root || path.startsWith(`${root}/`))) continue; // outside shipped subtrees
+    deleteSet.push(path);
+  }
+  return deleteSet;
+}
+
+function normalizeRel(p: string): string {
+  return p.replace(/\\/g, '/').replace(/^\.\//, '').replace(/^\/+/, '').replace(/\/+$/, '');
+}
+
+/** Translate a glob body (already normalized) into a RegExp source fragment. */
+function globToRegExpBody(pattern: string): string {
+  let out = '';
+  for (let i = 0; i < pattern.length; i++) {
+    const c = pattern[i];
+    if (c === undefined) continue;
+    if (c === '*') {
+      if (pattern[i + 1] === '*') {
+        // `**` — any depth. `a/**` must also match the bare root `a`, so when a
+        // literal `/` was just emitted, make it optional along with the rest.
+        i++;
+        let trailingSlash = false;
+        if (pattern[i + 1] === '/') {
+          i++;
+          trailingSlash = true;
+        }
+        if (out.endsWith('/')) {
+          out = `${out.slice(0, -1)}(?:/.*)?`;
+        } else if (trailingSlash) {
+          out += '(?:.*/)?';
+        } else {
+          out += '.*';
+        }
+      } else {
+        out += '[^/]*';
+      }
+    } else {
+      out += c.replace(/[.+?^${}()|[\]\\]/g, '\\$&');
+    }
+  }
+  return out;
+}
diff --git a/packages/mosaic/src/platform/file-ops.ts b/packages/mosaic/src/platform/file-ops.ts
index cce7887..55a689e 100644
--- a/packages/mosaic/src/platform/file-ops.ts
+++ b/packages/mosaic/src/platform/file-ops.ts
@@ -62,16 +62,28 @@ function rotateBackups(filePath: string): void {
 /**
  * Sync a source directory to a target, with optional preserve paths.
  * Replaces the rsync/cp logic from install.sh.
+ *
+ * `isOperatorOwned` is the #791 ownership guard: when supplied, any source path
+ * it flags as operator-owned is never copied (the framework must never write an
+ * operator path). Callers derive it from the shared framework manifest so the TS
+ * and bash sync paths obey one source of truth. This copy is non-destructive —
+ * it never deletes a target file — so honoring the guard is sufficient to leave
+ * operator config untouched.
  */
 export function syncDirectory(
   source: string,
   target: string,
-  options: { preserve?: string[]; excludeGit?: boolean } = {},
+  options: {
+    preserve?: string[];
+    excludeGit?: boolean;
+    isOperatorOwned?: (relPath: string) => boolean;
+  } = {},
 ): void {
   // Guard: source and target are the same directory — nothing to sync
   if (resolve(source) === resolve(target)) return;
 
   const preserveSet = new Set(options.preserve ?? []);
+  const isOperatorOwned = options.isOperatorOwned ?? (() => false);
 
   // Collect files from source
   function copyRecursive(src: string, dest: string, relBase: string): void {
@@ -86,7 +98,7 @@ export function syncDirectory(
       if (options.excludeGit && (dirName === '.git' || relPath.includes('/.git'))) return;
 
       // Skip preserved paths at top level
-      if (preserveSet.has(relPath) && existsSync(dest)) return;
+      if (relPath !== '' && preserveSet.has(relPath) && existsSync(dest)) return;
 
       mkdirSync(dest, { recursive: true });
       for (const entry of readdirSync(src)) {
@@ -101,6 +113,10 @@ export function syncDirectory(
       // Skip preserved files at top level
       if (preserveSet.has(relPath) && existsSync(dest)) return;
 
+      // #791: never write an operator-owned path (the framework owns only its
+      // own files; unknown paths resolve to operator and are skipped too).
+      if (isOperatorOwned(relPath)) return;
+
       mkdirSync(dirname(dest), { recursive: true });
       copyFileSync(src, dest);
     }
diff --git a/packages/mosaic/src/runtime/update-checker.ts b/packages/mosaic/src/runtime/update-checker.ts
index 492a0f2..6b1aee6 100644
--- a/packages/mosaic/src/runtime/update-checker.ts
+++ b/packages/mosaic/src/runtime/update-checker.ts
@@ -488,9 +488,13 @@ export function getInstallAllCommand(outdated: PackageUpdateResult[]): string {
 // `mosaic update` installs the new npm CLI but, on its own, leaves the framework
 // files in ~/.config/mosaic/ stale — so shipped launcher/runtime changes (e.g.
 // the agent-name export + native heartbeat) never ACTIVATE until a re-seed.
-// These helpers run the package's own install.sh in sync-only mode (the P4
-// data-safe reconcile: framework-owned overwrite + backup-once; SOUL/USER/
-// *.local/credentials preserved) and, opt-in, relaunch durable agents.
+// These helpers run the package's own install.sh in sync-only mode. The re-seed
+// is manifest-driven (#791): keep mode writes ONLY framework-owned paths from the
+// shared framework-manifest.txt and prunes only retired framework files inside
+// shipped subtrees — every operator path (SOUL/USER/*.local/credentials, fleet
+// roster + agents + backlog, and anything the manifest never anticipated) is
+// left byte-identical. Contract files are still reconciled (overwrite +
+// backup-once). Opt-in, this also relaunches durable agents.
 
 /** Resolve the framework/ directory bundled in the installed package. */
 export function resolveBundledFrameworkRoot(): string {