Model native FreeBSD world and kernel artifacts

docs/PROGRESS.md

@@ -2874,3 +2874,88 @@ Next recommended step:
 1. begin Phase 13.1 by modeling FreeBSD `world` and `kernel` as Fruix-managed build artifacts rather than host-copy packages
 2. use `/usr/src` as the initial source of truth on the builder side
 3. target the first bootable replacement for the current host-staged kernel and core runtime path
+
+## 2026-04-02 — Phase 13.1: modeled native FreeBSD world/kernel artifacts
+
+Completed work:
+
+- wrote the Phase 13.1 report:
+  - `docs/reports/phase13-native-base-model-freebsd.md`
+- added native FreeBSD base package objects in `modules/fruix/packages/freebsd.scm`:
+  - `freebsd-native-kernel`
+  - `freebsd-native-world`
+- added and exported:
+  - `freebsd-native-build-package?`
+- encoded the first native build parameters directly in those package definitions, including:
+  - `source-root=/usr/src`
+  - `target=amd64`
+  - `target-arch=amd64`
+  - `kernconf=GENERIC`
+  - make flags:
+    - `__MAKE_CONF=/dev/null`
+    - `SRCCONF=/dev/null`
+    - `SRC_ENV_CONF=/dev/null`
+    - `MK_DEBUG_FILES=no`
+    - `MK_TESTS=no`
+- the first native world artifact now also carries an explicit runtime-oriented prune list:
+  - `usr/share/doc`
+  - `usr/share/examples`
+  - `usr/share/info`
+  - `usr/share/man`
+  - `usr/tests`
+- extended `modules/fruix/system/freebsd.scm` so `materialize-freebsd-package` now understands:
+  - `copy-build-system`
+  - `freebsd-world-build-system`
+  - `freebsd-kernel-build-system`
+- added native-build identity/materialization helpers for:
+  - `/usr/src` source-tree identity
+  - `KERNCONF` path hashing
+  - build-root identity
+  - buildworld/buildkernel stamp handling
+  - staged installworld/installkernel materialization
+  - native build metadata files in store outputs
+- chose an `mtree`-based `/usr/src` identity for the first native output model using:
+  - `type`
+  - `link`
+  - `size`
+  - `mode`
+  - `sha256digest`
+- updated closure/image metadata modeling so the system can now distinguish:
+  - `host_base_stores`
+  - `native_base_stores`
+  - `fruix_runtime_stores`
+- updated profile/tree merging to skip private dotfile metadata from store outputs so native-build metadata does not leak into the merged runtime tree
+
+Validation:
+
+- confirmed the updated package/system modules still load after the native build-model additions
+- confirmed the new native package objects are present and classified as expected:
+  - `freebsd-native-kernel` reports build-system `freebsd-kernel-build-system`
+  - `freebsd-native-build-package? freebsd-native-world` returns `#t`
+- re-ran the existing host-copy regression check successfully:
+  - `tests/system/run-phase7-system-closure.sh`
+  - workdir: `/tmp/phase13-1-closure-1775164392`
+  - result: `PASS phase7-system-closure`
+
+Important findings:
+
+- Fruix now has a real model for FreeBSD base artifacts built from `/usr/src`; the project is no longer limited to describing the FreeBSD base only as host-copy packages
+- the first native identity story is explicit:
+  - `/usr/src` contributes through an `mtree`-based tree digest
+  - `KERNCONF` contributes through its resolved path hash
+  - selected make/build parameters are part of the manifest too
+- the repo can now describe a mixed system more honestly by separating:
+  - transitional host-staged base stores
+  - native base stores
+  - Fruix runtime stores
+
+Current assessment:
+
+- Phase 13.1 is complete
+- the next step is no longer architectural guesswork; it is concrete execution of the newly added native package/materialization path
+
+Next recommended step:
+
+1. build the first concrete `freebsd-native-kernel` and `freebsd-native-world` outputs from `/usr/src`
+2. inspect/document their staged contents in `/frx/store`
+3. then wire a bootable system closure/image around those native outputs