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, 41 deletions

diff --git a/llm/README.md b/llm/README.md
deleted file mode 100644
index 16c8f5b..0000000
--- a/llm/README.md
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@@ -1,41 +0,0 @@
-# LLM Notes Folder
-
-This folder is for comprehensive notes taken by AI agents after each major change to the codebase.
-
-## Purpose
-- Document learnings, insights, and decisions made during development
-- Track architectural changes, bug fixes, and feature implementations
-- Provide context for future agents or developers
-- Maintain a knowledge base of the project's evolution
-
-## Guidelines for Agents
-- Create a new markdown file for each major change (e.g., `2025-01-07-feature-x.md`)
-- Include: what was changed, why, challenges faced, solutions, and lessons learned
-- Be thorough but concise; aim for 200-500 words per note
-- Use consistent naming: `YYYY-MM-DD-brief-description.md`
-- Reference related files, commits, or issues
-
-## Template
-```
-# [Change Title]
-
-## Summary
-Brief overview of the change.
-
-## What Was Changed
-Detailed description of modifications.
-
-## Why This Change
-Rationale and benefits.
-
-## Challenges & Solutions
-Problems encountered and how they were resolved.
-
-## Learnings
-Key insights, best practices discovered, or future considerations.
-
-## Related
-- Files: list
-- Commits: hash
-- Issues: links
-```
\ No newline at end of file