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, 0 insertions, 33 deletions

diff --git a/llm/2026-01-07-Session-Changes-Summary.md b/llm/2026-01-07-Session-Changes-Summary.md
deleted file mode 100644
index d7ed6e3..0000000
--- a/llm/2026-01-07-Session-Changes-Summary.md
+++ /dev/null
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-# 2026-01-07-Session-Changes-Summary
-
-## Summary
-This note summarizes all changes made during the development session for the Nixtamal project, from initial darcs cloning to final git commit with comprehensive documentation.
-
-## What Was Changed
-1. **Project Conversion**: Migrated Nixtamal from Darcs to Git, preserving full history (140 commits, 9 tags)
-2. **Documentation Creation**: Created AGENTS.md with coding guidelines for AI agents
-3. **LLM Infrastructure**: Established ./llm/ folder for agent notes with README and template
-4. **README Updates**: Updated README.rst with current info and converted to README.asciidoc
-5. **Build Verification**: Confirmed builds and tests work correctly
-6. **Comprehensive Commit**: Created a detailed commit message documenting the entire project and session changes
-
-## Why This Change
-The session aimed to modernize the project's version control, enhance documentation for AI collaboration, and establish infrastructure for future development tracking. This ensures the project is accessible to broader development tools while maintaining its core functionality.
-
-## Challenges & Solutions
-- **Darcs to Git Conversion**: Challenge was ensuring complete history preservation. Solution: Used darcs convert export piped to git fast-import, verified commit/tag counts.
-- **Documentation Accuracy**: README had outdated info. Solution: Updated with current data and converted to AsciiDoc for better compatibility.
-- **Agent Guidelines**: No existing standards for AI coding. Solution: Created comprehensive AGENTS.md based on codebase analysis.
-- **Note Infrastructure**: Needed system for tracking learnings. Solution: Created ./llm/ with standardized template.
-
-## Learnings
-- Darcs conversion to Git is reliable using standard tools
-- AsciiDoc provides better markup flexibility than RST for technical docs
-- Establishing agent guidelines early improves consistency
-- Comprehensive commit messages serve as excellent project documentation
-- Nix-based builds require careful environment management
-
-## Related
-- Files: AGENTS.md, README.asciidoc, llm/README.md, llm/2026-01-07-Session-Changes-Summary.md
-- Commits: 7b55727 (comprehensive commit)
-- Issues: None (session work)
\ No newline at end of file