Port upstream patches: Cmdliner 2.x, lockfile auto-creation, schema upgrade, Fossil VCS

Ported from upstream darcs repository (v1.1.2):
- Cmdliner 2.x compatibility fixes (variable shadowing)
- Lockfile auto-creation when missing
- Schema upgrade command with backup/rollback
- Fossil VCS support (new VCS type)
- Clean up Cmdliner warning for unescaped $PWD

Files modified:
- lib/schema.ml (new): Schema versioning module
- lib/nixtamal.ml: Add upgrade function, Fossil meld support
- lib/error.ml: Add Fossil to prefetch_method, Upgrade error
- lib/input.ml: Add Fossil module, Kind variant
- lib/prefetch.ml: Add Fossil prefetch with SRI hash support
- lib/manifest.ml: Add Fossil codec
- lib/lockfile.ml: Add Fossil lockfile type
- lib/lock_loader.ml: Add Fossil feature flag
- lib/input_foreman.ml: Add Fossil display and prefetch check
- bin/cmd.ml: Cmdliner 2.x fixes, add Upgrade command
- bin/dune, lib/dune, test/dune: Deprecation flags

Builds successfully with all tests passing.

1 files changed, 26 insertions, 46 deletions

diff --git a/AGENTS.md b/AGENTS.md
index ef06157..6e2a2f6 100644
--- a/AGENTS.md
+++ b/AGENTS.md
@@ -1,24 +1,21 @@
 # AGENTS.md for nixtamal project
 
-## Project Overview
-**Nixtamal** is a Nix version pinning tool designed as an alternative/complement to flakes. It provides sophisticated dependency management with first-class support for Darcs, Pijul, and other VCS systems that flakes don't handle well.
+## Documentation
 
-**Strategic Position**: While nixtamal is philosophically an alternative to flakes, toastal is implementing dual support to provide ecosystem bridge capabilities while maintaining the project's core mission.
+User-facing documentation is in `README.asciidoc`. Agent notes go in `./llm/`.
 
 ## Build/Lint/Test Commands
 
 ### Traditional Nix Commands
-- Build: `dune build`
-- Test all: `dune runtest`
+- Build: `nix-build release.nix` or `nix build`
+- Test all: `nix-build release.nix -A check` or `dune runtest`
 - Run single test: `dune runtest --filter <test_name>` (use with alcotest test names)
 - Format: `dune build @fmt` (ocamlformat)
 - Clean: `dune clean`
 
-### Nix Integration Commands
-- Traditional build: `nix-build` or `nix-build release.nix`
-- Development shell: `nix-shell` or `nix-shell shell.nix`
-- Flake build (Phase 1+): `nix flake build` or `nix build .#nixtamal`
-- Flake shell (Phase 1+): `nix develop` or `nix shell .#devShell`
+### Nix Flake Commands
+- Build: `nix flake build` or `nix build .#nixtamal`
+- Dev shell: `nix develop` or `nix shell .#devShell`
 
 ## Code Style Guidelines
 - **Formatting**: Use ocamlformat (auto-formatted via dune @fmt)
@@ -31,47 +28,30 @@
 - **Line Length**: No strict limit, but aim for readability
 - **Pattern Matching**: Exhaustive, use `|` for clarity
 
-## Phase 1: Flake Integration Planning
+## Ongoing Integrations
 
-### Week 1 Objectives
-1. **Create `flake.nix`** with core outputs wrapping existing `release.nix`
-2. **Preserve existing infrastructure** as primary build method
-3. **Implement basic flake outputs**:
-   - `packages.${system}.default` (nixtamal package)
-   - `packages.${system}.nixtamal` (explicit package name)
-   - `devShells.${system}.default` (development environment)
-   - `checks.${system}` (test suite integration)
-   - `lib` outputs for ecosystem integration
+### Nilla Framework (In Progress)
 
-### Week 1 Deliverables
-- `flake.nix` with minimal working flake interface
-- `flake.lock` generation workflow
-- Documentation updates explaining dual approach
-- Testing both traditional and flake workflows
+Adding first-class support for https://github.com/nilla-nix/nilla[Nilla], a Nix framework with loaders and module system.
 
-### Strategic Constraints
-- **Maintain philosophical consistency**: Flakes as interface, not replacement
-- **Preserve existing workflows**: No breaking changes to current Nix infrastructure
-- **Complement over compete**: Position as bridge between traditional Nix and flake ecosystems
+**Status**: Types, codecs, and manifest serialization implemented. Prefetch not yet implemented.
+
+**Files modified**:
+- `lib/input.ml` - Nilla module with Reference type, Kind variant
+- `lib/manifest.ml` - KDL codec for Nilla input type
+- `lib/error.ml` - Added Nilla to prefetch_method, Not_implemented error
+- `lib/prefetch.ml` - Stub returning "not yet implemented"
+- `lib/input_foreman.ml` - Display and needs_prefetch logic
+- `lib/lock_loader.ml` - Feature constant
+- `lib/lockfile.ml` - Lockfile serialization
+- `lib/nixtamal.ml` - meld_input_with_lock support
+
+### Future Integrations
+- Additional VCS support as needed
+- Migration utilities (flakes, npins, niv)
 
 ## Agent Notes
 - After each major change, create comprehensive notes in `./llm/` folder
-- Use the template in `./llm/README.md`
+- Use the template in `./llm/README.md` (if present)
 - Document learnings, challenges, solutions, and insights for future reference
 - **Flake integration changes** should be specifically documented with strategic reasoning
-
-## Flake Integration Architecture
-
-### Design Principles
-1. **Wrapper Pattern**: flake.nix imports and wraps existing release.nix infrastructure
-2. **Dual Interface**: Both traditional Nix and flakes remain fully functional
-3. **Ecosystem Bridge**: Expose nixtamal capabilities to flake users without compromising core mission
-4. **Incremental Adoption**: Users can gradually engage with flakes without abandoning nixtamal
-
-### Key Architectural Decisions
-- Keep `nix/tamal/` system as primary input management
-- Use flakes only for build/packaging interface layer
-- Maintain backward compatibility with existing nixtamal projects
-- Provide migration utilities in future phases
-
-No Cursor or Copilot rules found.
\ No newline at end of file