apply mode: wire partition apply + mkfs; btrfs RAID1 flags and -f; UEFI detection and skip bios_boot when UEFI; sgdisk-based partition apply; update TODO and REGION markers

TODO.md

@@ -9,18 +9,30 @@ Conventions:
 
 Core execution
 
-- [ ] Add “apply mode” switch to orchestrator to perform destructive actions after preview validation
-  - Wire phase execution in [orchestrator.run(&Context)](src/orchestrator/run.rs:101): apply partitions → udev settle → mkfs → mount → maybe write fstab → build/write report
-  - Introduce a CLI flag (e.g. `--apply`) guarded by clear logs and safety checks (not preview)
-- [ ] Partition application (destructive) in [fn apply_partitions(...)](src/partition/plan.rs:287)
-  - Translate [PartitionPlan](src/partition/plan.rs:80) to sgdisk commands (create GPT, partitions in order with alignment and names)
-  - Enforce idempotency: skip if table already matches plan (or abort with explicit validation error)
-  - Ensure unique partition GUIDs; capture partition device paths and GUIDs for results
-  - Call [util::udev_settle()](src/util/mod.rs:128) after changes; robust error mapping to Error::Tool / Error::Partition
+- [-] Add “apply mode” switch to orchestrator to perform destructive actions after preview validation
+  - [x] Introduce CLI flag --apply guarded by clear logs and safety checks (not preview) [src/cli/args.rs](src/cli/args.rs)
+  - [x] Wire partition application and udev settle [orchestrator::run()](src/orchestrator/run.rs:1) → [partition::apply_partitions()](src/partition/plan.rs:1)
+  - [-] Wire mkfs → mount → maybe write fstab → build/write report [src/orchestrator/run.rs](src/orchestrator/run.rs)
+    - [x] Wire mkfs: plan_filesystems + make_filesystems [src/orchestrator/run.rs](src/orchestrator/run.rs) + [src/fs/plan.rs](src/fs/plan.rs)
+    - [ ] Wire mounts (plan/apply) [src/mount/ops.rs](src/mount/ops.rs)
+    - [ ] maybe write fstab [src/mount/ops.rs](src/mount/ops.rs)
+    - [ ] build/write report [src/report/state.rs](src/report/state.rs)
+- [x] Partition application (destructive) in [partition::apply_partitions()](src/partition/plan.rs:1)
+- [x] Boot mode detection and BIOS boot policy
+  - [x] Implement UEFI detection via /sys/firmware/efi: [is_efi_boot()](src/util/mod.rs:151)
+  - [x] Planner skips BIOS boot partition when UEFI-booted: [partition::plan_partitions()](src/partition/plan.rs:133)
+  - [ ] Future: revisit bootblock/bootloader specifics for BIOS vs EFI (confirm if any BIOS-targets require bios_boot) [docs/ARCHITECTURE.md](docs/ARCHITECTURE.md)
+  - [x] Translate [PartitionPlan](src/partition/plan.rs:1) to sgdisk commands (create GPT, partitions in order with alignment and names)
+  - [x] Enforce idempotency when required via [idempotency::is_empty_disk()](src/idempotency/mod.rs:1); abort on non-empty
+  - [x] Capture partition GUIDs, names, device paths via sgdisk -i parsing; map to PartitionResult
+  - [x] Call [util::udev_settle()](src/util/mod.rs:1) after changes; consistent Error::Tool/Error::Partition mapping
 - [-] Filesystem creation in [fn make_filesystems(...)](src/fs/plan.rs:182)
   - [x] Base mkfs implemented for vfat/btrfs/bcachefs (UUID capture via blkid)
-  - [ ] Apply btrfs raid profile from config (e.g., `-m raid1 -d raid1`) for [Topology::BtrfsRaid1](src/types.rs:29) and the desired profile in [struct BtrfsOptions](src/types.rs:89)
-  - [ ] Optionally map compression options for btrfs and bcachefs from config (e.g., `-O compress=zstd:3` or format-equivalent)
+  - [x] Apply btrfs RAID profile when topology requires it (multi-device): pass -m raid1 -d raid1 in mkfs.btrfs [src/fs/plan.rs](src/fs/plan.rs)
+  - [x] Force mkfs.btrfs in apply path with -f to handle leftover signatures from partial runs [src/fs/plan.rs](src/fs/plan.rs)
+  - [ ] Compression/tuning mapping from config
+    - [ ] btrfs: apply compression as mount options during mounting phase [src/mount/ops.rs](src/mount/ops.rs)
+    - [ ] bcachefs: map compression/checksum/cache_mode to format flags (deferred) [src/fs/plan.rs](src/fs/plan.rs)
   - [ ] Consider verifying UUID consistency across multi-device filesystems and improve error messages
 - [ ] Mount planning and application in [mount::ops](src/mount/ops.rs:1)
   - [ ] Implement [fn plan_mounts(...)](src/mount/ops.rs:68): map FsResult UUIDs into `/var/cache/{UUID}` using [cfg.mount.base_dir](src/types.rs:136), and synthesize options per FS kind
@@ -44,7 +56,7 @@ CLI, config, defaults
 - [x] Built-in sensible defaults (no YAML required) [src/config/loader.rs](src/config/loader.rs:320)
 - [x] Overlays from CLI: log level, file logging, fstab, removable policy, topology [src/config/loader.rs](src/config/loader.rs:247)
 - [x] Preview flags (`--show`, `--report`) and topology selection (`-t/--topology`) [src/cli/args.rs](src/cli/args.rs:55)
-- [ ] Add `--apply` flag to toggle execute mode and keep preview non-destructive by default [src/cli/args.rs](src/cli/args.rs:55)
+- [x] Add `--apply` flag to toggle execute mode and keep preview non-destructive by default [src/cli/args.rs](src/cli/args.rs)
 - [ ] Consider environment variable overlays [src/config/loader.rs](src/config/loader.rs:39)
 - [ ] Consider hidden/dev flags behind features (e.g., `--dry-run-verbose`, `--trace-io`) [src/cli/args.rs](src/cli/args.rs:26)