Fix tests

enroll/debian.py

@@ -63,6 +63,50 @@ def list_manual_packages() -> List[str]:
     return sorted(set(pkgs))
 
 
+def list_installed_packages() -> Dict[str, List[Dict[str, str]]]:
+    """Return mapping of installed package name -> installed instances.
+
+    Uses dpkg-query and is expected to work on Debian/Ubuntu-like systems.
+
+    Output format:
+      {"pkg": [{"version": "...", "arch": "..."}, ...], ...}
+    """
+
+    try:
+        p = subprocess.run(
+            [
+                "dpkg-query",
+                "-W",
+                "-f=${Package}\t${Version}\t${Architecture}\n",
+            ],
+            text=True,
+            capture_output=True,
+            check=False,
+        )  # nosec
+    except Exception:
+        return {}
+
+    out: Dict[str, List[Dict[str, str]]] = {}
+    for raw in (p.stdout or "").splitlines():
+        line = raw.strip("\n")
+        if not line:
+            continue
+        parts = line.split("\t")
+        if len(parts) < 3:
+            continue
+        name, ver, arch = parts[0].strip(), parts[1].strip(), parts[2].strip()
+        if not name:
+            continue
+        out.setdefault(name, []).append({"version": ver, "arch": arch})
+
+    # Stable ordering for deterministic JSON dumps.
+    for k in list(out.keys()):
+        out[k] = sorted(
+            out[k], key=lambda x: (x.get("arch") or "", x.get("version") or "")
+        )
+    return out
+
+
 def build_dpkg_etc_index(
     info_dir: str = "/var/lib/dpkg/info",
 ) -> Tuple[Set[str], Dict[str, str], Dict[str, Set[str]], Dict[str, List[str]]]:

enroll/diff.py

@@ -126,18 +126,62 @@ def _load_state(bundle_dir: Path) -> Dict[str, Any]:
         return json.load(f)
 
 
+def _packages_inventory(state: Dict[str, Any]) -> Dict[str, Any]:
+    return (state.get("inventory") or {}).get("packages") or {}
+
+
 def _all_packages(state: Dict[str, Any]) -> List[str]:
-    pkgs = set(state.get("manual_packages", []) or [])
+    return sorted(_packages_inventory(state).keys())
-    pkgs |= set(state.get("manual_packages_skipped", []) or [])
+
-    for s in state.get("services", []) or []:
+
-        for p in s.get("packages", []) or []:
+def _roles(state: Dict[str, Any]) -> Dict[str, Any]:
-            pkgs.add(p)
+    return state.get("roles") or {}
-    return sorted(pkgs)
+
+
+def _pkg_version_key(entry: Dict[str, Any]) -> Optional[str]:
+    """Return a stable string used for version comparison."""
+    installs = entry.get("installations") or []
+    if isinstance(installs, list) and installs:
+        parts: List[str] = []
+        for inst in installs:
+            if not isinstance(inst, dict):
+                continue
+            arch = str(inst.get("arch") or "")
+            ver = str(inst.get("version") or "")
+            if not ver:
+                continue
+            parts.append(f"{arch}:{ver}" if arch else ver)
+        if parts:
+            return "|".join(sorted(parts))
+    v = entry.get("version")
+    if v:
+        return str(v)
+    return None
+
+
+def _pkg_version_display(entry: Dict[str, Any]) -> Optional[str]:
+    v = entry.get("version")
+    if v:
+        return str(v)
+    installs = entry.get("installations") or []
+    if isinstance(installs, list) and installs:
+        parts: List[str] = []
+        for inst in installs:
+            if not isinstance(inst, dict):
+                continue
+            arch = str(inst.get("arch") or "")
+            ver = str(inst.get("version") or "")
+            if not ver:
+                continue
+            parts.append(f"{ver} ({arch})" if arch else ver)
+        if parts:
+            return ", ".join(sorted(parts))
+    return None
 
 
 def _service_units(state: Dict[str, Any]) -> Dict[str, Dict[str, Any]]:
     out: Dict[str, Dict[str, Any]] = {}
-    for s in state.get("services", []) or []:
+    for s in _roles(state).get("services") or []:
         unit = s.get("unit")
         if unit:
             out[str(unit)] = s
@@ -145,7 +189,7 @@ def _service_units(state: Dict[str, Any]) -> Dict[str, Dict[str, Any]]:
 
 
 def _users_by_name(state: Dict[str, Any]) -> Dict[str, Dict[str, Any]]:
-    users = (state.get("users") or {}).get("users") or []
+    users = (_roles(state).get("users") or {}).get("users") or []
     out: Dict[str, Dict[str, Any]] = {}
     for u in users:
         name = u.get("name")
@@ -167,43 +211,43 @@ class FileRec:
 
 def _iter_managed_files(state: Dict[str, Any]) -> Iterable[Tuple[str, Dict[str, Any]]]:
     # Services
-    for s in state.get("services", []) or []:
+    for s in _roles(state).get("services") or []:
         role = s.get("role_name") or "unknown"
         for mf in s.get("managed_files", []) or []:
             yield str(role), mf
 
     # Package roles
-    for p in state.get("package_roles", []) or []:
+    for p in _roles(state).get("packages") or []:
         role = p.get("role_name") or "unknown"
         for mf in p.get("managed_files", []) or []:
             yield str(role), mf
 
     # Users
-    u = state.get("users") or {}
+    u = _roles(state).get("users") or {}
     u_role = u.get("role_name") or "users"
     for mf in u.get("managed_files", []) or []:
         yield str(u_role), mf
 
     # apt_config
-    ac = state.get("apt_config") or {}
+    ac = _roles(state).get("apt_config") or {}
     ac_role = ac.get("role_name") or "apt_config"
     for mf in ac.get("managed_files", []) or []:
         yield str(ac_role), mf
 
     # etc_custom
-    ec = state.get("etc_custom") or {}
+    ec = _roles(state).get("etc_custom") or {}
     ec_role = ec.get("role_name") or "etc_custom"
     for mf in ec.get("managed_files", []) or []:
         yield str(ec_role), mf
 
     # usr_local_custom
-    ul = state.get("usr_local_custom") or {}
+    ul = _roles(state).get("usr_local_custom") or {}
     ul_role = ul.get("role_name") or "usr_local_custom"
     for mf in ul.get("managed_files", []) or []:
         yield str(ul_role), mf
 
     # extra_paths
-    xp = state.get("extra_paths") or {}
+    xp = _roles(state).get("extra_paths") or {}
     xp_role = xp.get("role_name") or "extra_paths"
     for mf in xp.get("managed_files", []) or []:
         yield str(xp_role), mf
@@ -261,12 +305,28 @@ def compare_harvests(
         old_state = _load_state(old_b.dir)
         new_state = _load_state(new_b.dir)
 
-        old_pkgs = set(_all_packages(old_state))
+        old_inv = _packages_inventory(old_state)
-        new_pkgs = set(_all_packages(new_state))
+        new_inv = _packages_inventory(new_state)
+
+        old_pkgs = set(old_inv.keys())
+        new_pkgs = set(new_inv.keys())
 
         pkgs_added = sorted(new_pkgs - old_pkgs)
         pkgs_removed = sorted(old_pkgs - new_pkgs)
 
+        pkgs_version_changed: List[Dict[str, Any]] = []
+        for pkg in sorted(old_pkgs & new_pkgs):
+            a = old_inv.get(pkg) or {}
+            b = new_inv.get(pkg) or {}
+            if _pkg_version_key(a) != _pkg_version_key(b):
+                pkgs_version_changed.append(
+                    {
+                        "package": pkg,
+                        "old": _pkg_version_display(a),
+                        "new": _pkg_version_display(b),
+                    }
+                )
+
         old_units = _service_units(old_state)
         new_units = _service_units(new_state)
         units_added = sorted(set(new_units) - set(old_units))
@@ -380,6 +440,7 @@ def compare_harvests(
             [
                 pkgs_added,
                 pkgs_removed,
+                pkgs_version_changed,
                 units_added,
                 units_removed,
                 units_changed,
@@ -413,7 +474,11 @@ def compare_harvests(
                 "state_mtime": _mtime_iso(new_b.state_path),
                 "host": (new_state.get("host") or {}).get("hostname"),
             },
-            "packages": {"added": pkgs_added, "removed": pkgs_removed},
+            "packages": {
+                "added": pkgs_added,
+                "removed": pkgs_removed,
+                "version_changed": pkgs_version_changed,
+            },
             "services": {
                 "enabled_added": units_added,
                 "enabled_removed": units_removed,
@@ -471,10 +536,13 @@ def _report_text(report: Dict[str, Any]) -> str:
     lines.append("\nPackages")
     lines.append(f"  added:   {len(pk.get('added', []) or [])}")
     lines.append(f"  removed: {len(pk.get('removed', []) or [])}")
+    lines.append(f"  version_changed: {len(pk.get('version_changed', []) or [])}")
     for p in pk.get("added", []) or []:
         lines.append(f"    + {p}")
     for p in pk.get("removed", []) or []:
         lines.append(f"    - {p}")
+    for ch in pk.get("version_changed", []) or []:
+        lines.append(f"    ~ {ch.get('package')}: {ch.get('old')} -> {ch.get('new')}")
 
     sv = report.get("services", {})
     lines.append("\nServices (enabled systemd units)")
@@ -542,6 +610,7 @@ def _report_text(report: Dict[str, Any]) -> str:
         [
             (pk.get("added") or []),
             (pk.get("removed") or []),
+            (pk.get("version_changed") or []),
             (sv.get("enabled_added") or []),
             (sv.get("enabled_removed") or []),
             (sv.get("changed") or []),
@@ -578,6 +647,12 @@ def _report_markdown(report: Dict[str, Any]) -> str:
     for p in pk.get("removed", []) or []:
         out.append(f"  - `- {p}`\n")
 
+    out.append(f"- Version changed: {len(pk.get('version_changed', []) or [])}\n")
+    for ch in pk.get("version_changed", []) or []:
+        out.append(
+            f"  - `~ {ch.get('package')}`: `{ch.get('old')}` → `{ch.get('new')}`\n"
+        )
+
     sv = report.get("services", {})
     out.append("## Services (enabled systemd units)\n")
     if sv.get("enabled_added"):
@@ -672,6 +747,7 @@ def _report_markdown(report: Dict[str, Any]) -> str:
         [
             (pk.get("added") or []),
             (pk.get("removed") or []),
+            (pk.get("version_changed") or []),
             (sv.get("enabled_added") or []),
             (sv.get("enabled_removed") or []),
             (sv.get("changed") or []),

enroll/harvest.py

@@ -5,6 +5,7 @@ import json
 import os
 import re
 import shutil
+import time
 from dataclasses import dataclass, asdict
 from typing import Dict, List, Optional, Set
 
@@ -1481,9 +1482,60 @@ def harvest(
         notes=extra_notes,
     )
 
+    # -------------------------
+    # Inventory: packages (SBOM-ish)
+    # -------------------------
+    installed = backend.installed_packages() or {}
+
+    manual_set: Set[str] = set(manual_pkgs or [])
+
+    pkg_units: Dict[str, Set[str]] = {}
+    pkg_roles_map: Dict[str, Set[str]] = {}
+
+    for svc in service_snaps:
+        for p in svc.packages:
+            pkg_units.setdefault(p, set()).add(svc.unit)
+            pkg_roles_map.setdefault(p, set()).add(svc.role_name)
+
+    pkg_role_names: Dict[str, List[str]] = {}
+    for ps in pkg_snaps:
+        pkg_roles_map.setdefault(ps.package, set()).add(ps.role_name)
+        pkg_role_names.setdefault(ps.package, []).append(ps.role_name)
+
+    pkg_names: Set[str] = set()
+    pkg_names |= manual_set
+    pkg_names |= set(pkg_units.keys())
+    pkg_names |= {ps.package for ps in pkg_snaps}
+
+    packages_inventory: Dict[str, Dict[str, object]] = {}
+    for pkg in sorted(pkg_names):
+        installs = installed.get(pkg, []) or []
+        arches = sorted({i.get("arch") for i in installs if i.get("arch")})
+        vers = sorted({i.get("version") for i in installs if i.get("version")})
+        version: Optional[str] = vers[0] if len(vers) == 1 else None
+
+        observed: List[Dict[str, str]] = []
+        if pkg in manual_set:
+            observed.append({"kind": "user_installed"})
+        for unit in sorted(pkg_units.get(pkg, set())):
+            observed.append({"kind": "systemd_unit", "ref": unit})
+        for rn in sorted(set(pkg_role_names.get(pkg, []))):
+            observed.append({"kind": "package_role", "ref": rn})
+
+        roles = sorted(pkg_roles_map.get(pkg, set()))
+
+        packages_inventory[pkg] = {
+            "version": version,
+            "arches": arches,
+            "installations": installs,
+            "observed_via": observed,
+            "roles": roles,
+        }
+
     state = {
         "enroll": {
             "version": get_enroll_version(),
+            "harvest_time": time.time_ns(),
         },
         "host": {
             "hostname": os.uname().nodename,
@@ -1491,16 +1543,19 @@ def harvest(
             "pkg_backend": backend.name,
             "os_release": platform.os_release,
         },
+        "inventory": {
+            "packages": packages_inventory,
+        },
+        "roles": {
             "users": asdict(users_snapshot),
             "services": [asdict(s) for s in service_snaps],
-        "manual_packages": manual_pkgs,
+            "packages": [asdict(p) for p in pkg_snaps],
-        "manual_packages_skipped": manual_pkgs_skipped,
-        "package_roles": [asdict(p) for p in pkg_snaps],
             "apt_config": asdict(apt_config_snapshot),
             "dnf_config": asdict(dnf_config_snapshot),
             "etc_custom": asdict(etc_custom_snapshot),
             "usr_local_custom": asdict(usr_local_custom_snapshot),
             "extra_paths": asdict(extra_paths_snapshot),
+        },
     }
 
     state_path = os.path.join(bundle_dir, "state.json")

enroll/manifest.py

@@ -271,9 +271,7 @@ def _write_hostvars(site_root: str, fqdn: str, role: str, data: Dict[str, Any])
 
     merged = _merge_mappings_overwrite(existing_map, data)
 
-    out = "# Generated by enroll (host-specific vars)\n---\n" + _yaml_dump_mapping(
+    out = "---\n" + _yaml_dump_mapping(merged, sort_keys=True)
-        merged, sort_keys=True
-    )
     with open(path, "w", encoding="utf-8") as f:
         f.write(out)
 
@@ -392,9 +390,7 @@ def _render_generic_files_tasks(
     # Using first_found makes roles work in both modes:
     # - site-mode: inventory/host_vars/<host>/<role>/.files/...
     # - non-site: roles/<role>/files/...
-    return f"""# Generated by enroll
+    return f"""- name: Deploy any systemd unit files (templates)
-
-- name: Deploy any systemd unit files (templates)
   ansible.builtin.template:
     src: "{{{{ item.src_rel }}}}.j2"
     dest: "{{{{ item.dest }}}}"
@@ -477,9 +473,7 @@ def _render_install_packages_tasks(role: str, var_prefix: str) -> str:
     generic `package` module. This keeps generated roles usable on both
     Debian-like and RPM-like systems.
     """
-    return f"""# Generated by enroll
+    return f"""- name: Install packages for {role} (APT)
-
-- name: Install packages for {role} (APT)
   ansible.builtin.apt:
     name: "{{{{ {var_prefix}_packages | default([]) }}}}"
     state: present
@@ -672,14 +666,16 @@ def _manifest_from_bundle_dir(
     with open(state_path, "r", encoding="utf-8") as f:
         state = json.load(f)
 
-    services: List[Dict[str, Any]] = state.get("services", [])
+    roles: Dict[str, Any] = state.get("roles") or {}
-    package_roles: List[Dict[str, Any]] = state.get("package_roles", [])
+
-    users_snapshot: Dict[str, Any] = state.get("users", {})
+    services: List[Dict[str, Any]] = roles.get("services", [])
-    apt_config_snapshot: Dict[str, Any] = state.get("apt_config", {})
+    package_roles: List[Dict[str, Any]] = roles.get("packages", [])
-    dnf_config_snapshot: Dict[str, Any] = state.get("dnf_config", {})
+    users_snapshot: Dict[str, Any] = roles.get("users", {})
-    etc_custom_snapshot: Dict[str, Any] = state.get("etc_custom", {})
+    apt_config_snapshot: Dict[str, Any] = roles.get("apt_config", {})
-    usr_local_custom_snapshot: Dict[str, Any] = state.get("usr_local_custom", {})
+    dnf_config_snapshot: Dict[str, Any] = roles.get("dnf_config", {})
-    extra_paths_snapshot: Dict[str, Any] = state.get("extra_paths", {})
+    etc_custom_snapshot: Dict[str, Any] = roles.get("etc_custom", {})
+    usr_local_custom_snapshot: Dict[str, Any] = roles.get("usr_local_custom", {})
+    extra_paths_snapshot: Dict[str, Any] = roles.get("extra_paths", {})
 
     site_mode = fqdn is not None and fqdn != ""
 
@@ -839,7 +835,6 @@ def _manifest_from_bundle_dir(
 
         # tasks (data-driven)
         users_tasks = """---
-# Generated by enroll
 
 - name: Ensure groups exist
   ansible.builtin.group:
@@ -996,7 +991,7 @@ Generated non-system user accounts and SSH public material.
         else:
             _write_role_defaults(role_dir, vars_map)
 
-        tasks = """---\n""" + _render_generic_files_tasks(
+        tasks = "---\n" + _render_generic_files_tasks(
             var_prefix, include_restart_notify=False
         )
         with open(
@@ -1298,7 +1293,7 @@ DNF/YUM configuration harvested from the system (repos, config files, and RPM GP
         else:
             _write_role_defaults(role_dir, vars_map)
 
-        tasks = """---\n""" + _render_generic_files_tasks(
+        tasks = "---\n" + _render_generic_files_tasks(
             var_prefix, include_restart_notify=False
         )
         with open(
@@ -1664,8 +1659,7 @@ User-requested extra file harvesting.
         )
 
         task_parts.append(
-            f"""
+            f"""- name: Probe whether systemd unit exists and is manageable
-- name: Probe whether systemd unit exists and is manageable
   ansible.builtin.systemd:
     name: "{{{{ {var_prefix}_unit_name }}}}"
   check_mode: true

enroll/platform.py

@@ -81,6 +81,17 @@ class PackageBackend:
     def list_manual_packages(self) -> List[str]:  # pragma: no cover
         raise NotImplementedError
 
+    def installed_packages(self) -> Dict[str, List[Dict[str, str]]]:  # pragma: no cover
+        """Return mapping of package name -> installed instances.
+
+        Each instance is a dict with at least:
+          - version: package version string
+          - arch: architecture string
+
+        Backends should be best-effort and return an empty mapping on failure.
+        """
+        raise NotImplementedError
+
     def build_etc_index(
         self,
     ) -> Tuple[
@@ -121,6 +132,11 @@ class DpkgBackend(PackageBackend):
 
         return list_manual_packages()
 
+    def installed_packages(self) -> Dict[str, List[Dict[str, str]]]:
+        from .debian import list_installed_packages
+
+        return list_installed_packages()
+
     def build_etc_index(self):
         from .debian import build_dpkg_etc_index
 
@@ -194,6 +210,11 @@ class RpmBackend(PackageBackend):
 
         return list_manual_packages()
 
+    def installed_packages(self) -> Dict[str, List[Dict[str, str]]]:
+        from .rpm import list_installed_packages
+
+        return list_installed_packages()
+
     def build_etc_index(self):
         from .rpm import build_rpm_etc_index
 

enroll/rpm.py

@@ -104,7 +104,7 @@ def list_manual_packages() -> List[str]:
                 if pkgs:
                     return _dedupe(pkgs)
 
-        # Fallback: human-oriented output.
+        # Fallback
         rc, out = _run(
             ["dnf", "-q", "history", "userinstalled"], allow_fail=True, merge_err=True
         )
@@ -142,6 +142,63 @@ def list_manual_packages() -> List[str]:
     return []
 
 
+def list_installed_packages() -> Dict[str, List[Dict[str, str]]]:
+    """Return mapping of installed package name -> installed instances.
+
+    Uses `rpm -qa` and is expected to work on RHEL/Fedora-like systems.
+
+    Output format:
+      {"pkg": [{"version": "...", "arch": "..."}, ...], ...}
+
+    The version string is formatted as:
+      - "<version>-<release>" for typical packages
+      - "<epoch>:<version>-<release>" if a non-zero epoch is present
+    """
+
+    try:
+        _, out = _run(
+            [
+                "rpm",
+                "-qa",
+                "--qf",
+                "%{NAME}\t%{EPOCHNUM}\t%{VERSION}\t%{RELEASE}\t%{ARCH}\n",
+            ],
+            allow_fail=False,
+            merge_err=True,
+        )
+    except Exception:
+        return {}
+
+    pkgs: Dict[str, List[Dict[str, str]]] = {}
+    for raw in (out or "").splitlines():
+        line = raw.strip("\n")
+        if not line:
+            continue
+        parts = line.split("\t")
+        if len(parts) < 5:
+            continue
+        name, epoch, ver, rel, arch = [p.strip() for p in parts[:5]]
+        if not name or not ver:
+            continue
+
+        # Normalise epoch.
+        epoch = epoch.strip()
+        if epoch.lower() in ("(none)", "none", ""):
+            epoch = "0"
+
+        v = f"{ver}-{rel}" if rel else ver
+        if epoch and epoch.isdigit() and epoch != "0":
+            v = f"{epoch}:{v}"
+
+        pkgs.setdefault(name, []).append({"version": v, "arch": arch})
+
+    for k in list(pkgs.keys()):
+        pkgs[k] = sorted(
+            pkgs[k], key=lambda x: (x.get("arch") or "", x.get("version") or "")
+        )
+    return pkgs
+
+
 def _walk_etc_files() -> List[str]:
     out: List[str] = []
     for dirpath, _, filenames in os.walk("/etc"):

tests/test_diff_usr_local_custom.py

@@ -18,7 +18,20 @@ def test_diff_includes_usr_local_custom_files(tmp_path: Path):
     new = tmp_path / "new"
 
     old_state = {
-        "host": {"hostname": "h1", "os": "debian"},
+        "schema_version": 3,
+        "host": {"hostname": "h1", "os": "debian", "pkg_backend": "dpkg"},
+        "inventory": {
+            "packages": {
+                "curl": {
+                    "version": "1.0",
+                    "arches": [],
+                    "installations": [{"version": "1.0", "arch": "amd64"}],
+                    "observed_via": [{"kind": "user_installed"}],
+                    "roles": [],
+                }
+            }
+        },
+        "roles": {
             "users": {
                 "role_name": "users",
                 "users": [],
@@ -27,9 +40,13 @@ def test_diff_includes_usr_local_custom_files(tmp_path: Path):
                 "notes": [],
             },
             "services": [],
-        "package_roles": [],
+            "packages": [],
-        "manual_packages": ["curl"],
+            "apt_config": {
-        "manual_packages_skipped": [],
+                "role_name": "apt_config",
+                "managed_files": [],
+                "excluded": [],
+                "notes": [],
+            },
             "etc_custom": {
                 "role_name": "etc_custom",
                 "managed_files": [],
@@ -51,10 +68,33 @@ def test_diff_includes_usr_local_custom_files(tmp_path: Path):
                 "excluded": [],
                 "notes": [],
             },
+            "extra_paths": {
+                "role_name": "extra_paths",
+                "include_patterns": [],
+                "exclude_patterns": [],
+                "managed_files": [],
+                "excluded": [],
+                "notes": [],
+            },
+        },
     }
+
     new_state = {
         **old_state,
-        "manual_packages": ["curl", "htop"],
+        "inventory": {
+            "packages": {
+                **old_state["inventory"]["packages"],
+                "htop": {
+                    "version": "3.0",
+                    "arches": [],
+                    "installations": [{"version": "3.0", "arch": "amd64"}],
+                    "observed_via": [{"kind": "user_installed"}],
+                    "roles": [],
+                },
+            }
+        },
+        "roles": {
+            **old_state["roles"],
             "usr_local_custom": {
                 "role_name": "usr_local_custom",
                 "managed_files": [
@@ -78,6 +118,7 @@ def test_diff_includes_usr_local_custom_files(tmp_path: Path):
                 "excluded": [],
                 "notes": [],
             },
+        },
     }
 
     _write_bundle(

tests/test_harvest.py

@@ -30,6 +30,7 @@ class FakeBackend:
         owner_fn,
         modified_by_pkg: dict[str, dict[str, str]] | None = None,
         pkg_config_prefixes: tuple[str, ...] = ("/etc/apt/",),
+        installed: dict[str, list[dict[str, str]]] | None = None,
     ):
         self.name = name
         self.pkg_config_prefixes = pkg_config_prefixes
@@ -40,6 +41,7 @@ class FakeBackend:
         self._manual = manual_pkgs
         self._owner_fn = owner_fn
         self._modified_by_pkg = modified_by_pkg or {}
+        self._installed = installed or {}
 
     def build_etc_index(self):
         return (
@@ -55,6 +57,14 @@ class FakeBackend:
     def list_manual_packages(self):
         return list(self._manual)
 
+    def installed_packages(self):
+        """Return mapping package -> installations.
+
+        The real backends return:
+          {"pkg": [{"version": "...", "arch": "..."}, ...]}
+        """
+        return dict(self._installed)
+
     def specific_paths_for_hints(self, hints: set[str]):
         return []
 
@@ -214,26 +224,36 @@ def test_harvest_dedup_manual_packages_and_builds_etc_custom(
     state_path = h.harvest(str(bundle), policy=AllowAllPolicy())
     st = json.loads(Path(state_path).read_text(encoding="utf-8"))
 
-    assert "openvpn" in st["manual_packages"]
+    inv = st["inventory"]["packages"]
-    assert "curl" in st["manual_packages"]
+    assert "openvpn" in inv
-    assert "openvpn" in st["manual_packages_skipped"]
+    assert "curl" in inv
-    assert all(pr["package"] != "openvpn" for pr in st["package_roles"])
+
-    assert any(pr["package"] == "curl" for pr in st["package_roles"])
+    # openvpn is managed by the service role, so it should NOT appear as a package role.
+    pkg_roles = st["roles"]["packages"]
+    assert all(pr["package"] != "openvpn" for pr in pkg_roles)
+    assert any(pr["package"] == "curl" for pr in pkg_roles)
+
+    # Inventory provenance: openvpn should be observed via systemd unit.
+    openvpn_obs = inv["openvpn"]["observed_via"]
+    assert any(
+        o.get("kind") == "systemd_unit" and o.get("ref") == "openvpn.service"
+        for o in openvpn_obs
+    )
 
     # Service role captured modified conffile
-    svc = st["services"][0]
+    svc = st["roles"]["services"][0]
     assert svc["unit"] == "openvpn.service"
     assert "openvpn" in svc["packages"]
     assert any(mf["path"] == "/etc/openvpn/server.conf" for mf in svc["managed_files"])
 
     # Unowned /etc/default/keyboard is attributed to etc_custom only
-    etc_custom = st["etc_custom"]
+    etc_custom = st["roles"]["etc_custom"]
     assert any(
         mf["path"] == "/etc/default/keyboard" for mf in etc_custom["managed_files"]
     )
 
     # /usr/local content is attributed to usr_local_custom
-    ul = st["usr_local_custom"]
+    ul = st["roles"]["usr_local_custom"]
     assert any(mf["path"] == "/usr/local/etc/myapp.conf" for mf in ul["managed_files"])
     assert any(mf["path"] == "/usr/local/bin/myscript" for mf in ul["managed_files"])
     assert all(mf["path"] != "/usr/local/bin/readme.txt" for mf in ul["managed_files"])
@@ -338,10 +358,12 @@ def test_shared_cron_snippet_prefers_matching_role_over_lexicographic(
     st = json.loads(Path(state_path).read_text(encoding="utf-8"))
 
     # Cron snippet should end up attached to the ntpsec role, not apparmor.
-    svc_ntpsec = next(s for s in st["services"] if s["role_name"] == "ntpsec")
+    svc_ntpsec = next(s for s in st["roles"]["services"] if s["role_name"] == "ntpsec")
     assert any(mf["path"] == "/etc/cron.d/ntpsec" for mf in svc_ntpsec["managed_files"])
 
-    svc_apparmor = next(s for s in st["services"] if s["role_name"] == "apparmor")
+    svc_apparmor = next(
+        s for s in st["roles"]["services"] if s["role_name"] == "apparmor"
+    )
     assert all(
         mf["path"] != "/etc/cron.d/ntpsec" for mf in svc_apparmor["managed_files"]
     )

tests/test_jinjaturtle.py

@@ -24,7 +24,20 @@ def test_manifest_uses_jinjaturtle_templates_and_does_not_copy_raw(
     )
 
     state = {
-        "host": {"hostname": "test", "os": "debian"},
+        "schema_version": 3,
+        "host": {"hostname": "test", "os": "debian", "pkg_backend": "dpkg"},
+        "inventory": {
+            "packages": {
+                "foo": {
+                    "version": "1.0",
+                    "arches": [],
+                    "installations": [{"version": "1.0", "arch": "amd64"}],
+                    "observed_via": [{"kind": "systemd_unit", "ref": "foo.service"}],
+                    "roles": ["foo"],
+                }
+            }
+        },
+        "roles": {
             "users": {
                 "role_name": "users",
                 "users": [],
@@ -32,12 +45,6 @@ def test_manifest_uses_jinjaturtle_templates_and_does_not_copy_raw(
                 "excluded": [],
                 "notes": [],
             },
-        "etc_custom": {
-            "role_name": "etc_custom",
-            "managed_files": [],
-            "excluded": [],
-            "notes": [],
-        },
             "services": [
                 {
                     "unit": "foo.service",
@@ -61,7 +68,34 @@ def test_manifest_uses_jinjaturtle_templates_and_does_not_copy_raw(
                     "notes": [],
                 }
             ],
-        "package_roles": [],
+            "packages": [],
+            "apt_config": {
+                "role_name": "apt_config",
+                "managed_files": [],
+                "excluded": [],
+                "notes": [],
+            },
+            "etc_custom": {
+                "role_name": "etc_custom",
+                "managed_files": [],
+                "excluded": [],
+                "notes": [],
+            },
+            "usr_local_custom": {
+                "role_name": "usr_local_custom",
+                "managed_files": [],
+                "excluded": [],
+                "notes": [],
+            },
+            "extra_paths": {
+                "role_name": "extra_paths",
+                "include_patterns": [],
+                "exclude_patterns": [],
+                "managed_files": [],
+                "excluded": [],
+                "notes": [],
+            },
+        },
     }
 
     bundle.mkdir(parents=True, exist_ok=True)

tests/test_manifest.py

@@ -13,7 +13,27 @@ def test_manifest_writes_roles_and_playbook_with_clean_when(tmp_path: Path):
     )
 
     state = {
-        "host": {"hostname": "test", "os": "debian"},
+        "schema_version": 3,
+        "host": {"hostname": "test", "os": "debian", "pkg_backend": "dpkg"},
+        "inventory": {
+            "packages": {
+                "foo": {
+                    "version": "1.0",
+                    "arches": [],
+                    "installations": [{"version": "1.0", "arch": "amd64"}],
+                    "observed_via": [{"kind": "systemd_unit", "ref": "foo.service"}],
+                    "roles": ["foo"],
+                },
+                "curl": {
+                    "version": "8.0",
+                    "arches": [],
+                    "installations": [{"version": "8.0", "arch": "amd64"}],
+                    "observed_via": [{"kind": "package_role", "ref": "curl"}],
+                    "roles": ["curl"],
+                },
+            }
+        },
+        "roles": {
             "users": {
                 "role_name": "users",
                 "users": [
@@ -32,6 +52,50 @@ def test_manifest_writes_roles_and_playbook_with_clean_when(tmp_path: Path):
                 "excluded": [],
                 "notes": [],
             },
+            "services": [
+                {
+                    "unit": "foo.service",
+                    "role_name": "foo",
+                    "packages": ["foo"],
+                    "active_state": "inactive",
+                    "sub_state": "dead",
+                    "unit_file_state": "enabled",
+                    "condition_result": "no",
+                    "managed_files": [
+                        {
+                            "path": "/etc/foo.conf",
+                            "src_rel": "etc/foo.conf",
+                            "owner": "root",
+                            "group": "root",
+                            "mode": "0644",
+                            "reason": "modified_conffile",
+                        }
+                    ],
+                    "excluded": [],
+                    "notes": [],
+                }
+            ],
+            "packages": [
+                {
+                    "package": "curl",
+                    "role_name": "curl",
+                    "managed_files": [],
+                    "excluded": [],
+                    "notes": [],
+                }
+            ],
+            "apt_config": {
+                "role_name": "apt_config",
+                "managed_files": [],
+                "excluded": [],
+                "notes": [],
+            },
+            "dnf_config": {
+                "role_name": "dnf_config",
+                "managed_files": [],
+                "excluded": [],
+                "notes": [],
+            },
             "etc_custom": {
                 "role_name": "etc_custom",
                 "managed_files": [
@@ -70,38 +134,15 @@ def test_manifest_writes_roles_and_playbook_with_clean_when(tmp_path: Path):
                 "excluded": [],
                 "notes": [],
             },
-        "services": [
+            "extra_paths": {
-            {
+                "role_name": "extra_paths",
-                "unit": "foo.service",
+                "include_patterns": [],
-                "role_name": "foo",
+                "exclude_patterns": [],
-                "packages": ["foo"],
-                "active_state": "inactive",
-                "sub_state": "dead",
-                "unit_file_state": "enabled",
-                "condition_result": "no",
-                "managed_files": [
-                    {
-                        "path": "/etc/foo.conf",
-                        "src_rel": "etc/foo.conf",
-                        "owner": "root",
-                        "group": "root",
-                        "mode": "0644",
-                        "reason": "modified_conffile",
-                    }
-                ],
-                "excluded": [],
-                "notes": [],
-            }
-        ],
-        "package_roles": [
-            {
-                "package": "curl",
-                "role_name": "curl",
                 "managed_files": [],
                 "excluded": [],
                 "notes": [],
-            }
+            },
-        ],
+        },
     }
 
     bundle.mkdir(parents=True, exist_ok=True)
@@ -189,7 +230,20 @@ def test_manifest_site_mode_creates_host_inventory_and_raw_files(tmp_path: Path)
     )
 
     state = {
-        "host": {"hostname": "test", "os": "debian"},
+        "schema_version": 3,
+        "host": {"hostname": "test", "os": "debian", "pkg_backend": "dpkg"},
+        "inventory": {
+            "packages": {
+                "foo": {
+                    "version": "1.0",
+                    "arches": [],
+                    "installations": [{"version": "1.0", "arch": "amd64"}],
+                    "observed_via": [{"kind": "systemd_unit", "ref": "foo.service"}],
+                    "roles": ["foo"],
+                }
+            }
+        },
+        "roles": {
             "users": {
                 "role_name": "users",
                 "users": [],
@@ -197,6 +251,42 @@ def test_manifest_site_mode_creates_host_inventory_and_raw_files(tmp_path: Path)
                 "excluded": [],
                 "notes": [],
             },
+            "services": [
+                {
+                    "unit": "foo.service",
+                    "role_name": "foo",
+                    "packages": ["foo"],
+                    "active_state": "active",
+                    "sub_state": "running",
+                    "unit_file_state": "enabled",
+                    "condition_result": "yes",
+                    "managed_files": [
+                        {
+                            "path": "/etc/foo.conf",
+                            "src_rel": "etc/foo.conf",
+                            "owner": "root",
+                            "group": "root",
+                            "mode": "0644",
+                            "reason": "modified_conffile",
+                        }
+                    ],
+                    "excluded": [],
+                    "notes": [],
+                }
+            ],
+            "packages": [],
+            "apt_config": {
+                "role_name": "apt_config",
+                "managed_files": [],
+                "excluded": [],
+                "notes": [],
+            },
+            "dnf_config": {
+                "role_name": "dnf_config",
+                "managed_files": [],
+                "excluded": [],
+                "notes": [],
+            },
             "etc_custom": {
                 "role_name": "etc_custom",
                 "managed_files": [
@@ -227,30 +317,15 @@ def test_manifest_site_mode_creates_host_inventory_and_raw_files(tmp_path: Path)
                 "excluded": [],
                 "notes": [],
             },
-        "services": [
+            "extra_paths": {
-            {
+                "role_name": "extra_paths",
-                "unit": "foo.service",
+                "include_patterns": [],
-                "role_name": "foo",
+                "exclude_patterns": [],
-                "packages": ["foo"],
+                "managed_files": [],
-                "active_state": "active",
-                "sub_state": "running",
-                "unit_file_state": "enabled",
-                "condition_result": "yes",
-                "managed_files": [
-                    {
-                        "path": "/etc/foo.conf",
-                        "src_rel": "etc/foo.conf",
-                        "owner": "root",
-                        "group": "root",
-                        "mode": "0644",
-                        "reason": "modified_conffile",
-                    }
-                ],
                 "excluded": [],
                 "notes": [],
-            }
+            },
-        ],
+        },
-        "package_roles": [],
     }
 
     bundle.mkdir(parents=True, exist_ok=True)
@@ -337,7 +412,20 @@ def test_manifest_includes_dnf_config_role_when_present(tmp_path: Path):
     )
 
     state = {
+        "schema_version": 3,
         "host": {"hostname": "test", "os": "redhat", "pkg_backend": "rpm"},
+        "inventory": {
+            "packages": {
+                "dnf": {
+                    "version": "4.0",
+                    "arches": [],
+                    "installations": [{"version": "4.0", "arch": "x86_64"}],
+                    "observed_via": [{"kind": "dnf_config"}],
+                    "roles": [],
+                }
+            }
+        },
+        "roles": {
             "users": {
                 "role_name": "users",
                 "users": [],
@@ -346,9 +434,7 @@ def test_manifest_includes_dnf_config_role_when_present(tmp_path: Path):
                 "notes": [],
             },
             "services": [],
-        "package_roles": [],
+            "packages": [],
-        "manual_packages": [],
-        "manual_packages_skipped": [],
             "apt_config": {
                 "role_name": "apt_config",
                 "managed_files": [],
@@ -390,6 +476,7 @@ def test_manifest_includes_dnf_config_role_when_present(tmp_path: Path):
                 "excluded": [],
                 "notes": [],
             },
+        },
     }
 
     bundle.mkdir(parents=True, exist_ok=True)