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.

3 files changed, 78 insertions, 8 deletions

diff --git a/bin/cmd.ml b/bin/cmd.ml
index a411f43..533584d 100644
--- a/bin/cmd.ml
+++ b/bin/cmd.ml
@@ -29,7 +29,7 @@ module Global = struct
 			& info
 				["directory"]
 				~env
-				~doc: "Working directory for Nixtamal-related files (default: $PWD/nix/tamal)"
+				~doc: "Working directory for Nixtamal-related files (default: \\$PWD/nix/tamal)"
 				~docv: "PATH"
 		)
 
@@ -186,8 +186,9 @@ module Set_up = struct
 					$ nixpkgs_revision_arg
 				)
 		in
+		let eio_env = env in
 		Term.(
-			const (fun glb -> Global.run ~env glb @@ run)
+			const (fun glb -> Global.run ~env: eio_env glb @@ run)
 			$ Global.args
 			$ nixpkgs_arg
 		)
@@ -210,8 +211,9 @@ module Check_soundness = struct
 
 	let term ~env =
 		let open Cmdliner in
+		let eio_env = env in
 		Term.(
-			const (fun glb -> Global.run ~env glb @@ run)
+			const (fun glb -> Global.run ~env: eio_env glb @@ run)
 			$ Global.args
 		)
 
@@ -233,8 +235,9 @@ module Tweak = struct
 
 	let term ~env =
 		let open Cmdliner in
+		let eio_env = env in
 		Term.(
-			const (fun glb -> Global.run ~env glb @@ run)
+			const (fun glb -> Global.run ~env: eio_env glb @@ run)
 			$ Global.args
 		)
 
@@ -255,8 +258,9 @@ module Show = struct
 
 	let term ~env =
 		let open Cmdliner in
+		let eio_env = env in
 		Term.(
-			const (fun glb -> Global.run ~env glb @@ run)
+			const (fun glb -> Global.run ~env: eio_env glb @@ run)
 			$ Global.args
 		)
 
@@ -291,8 +295,9 @@ module Lock = struct
 				& info [] ~docv: "INPUT_NAME" ~doc: "Input names to lock (if already locked, will skip)."
 			)
 		in
+		let eio_env = env in
 		Term.(
-			const (fun glb force -> Global.run ~env glb @@ run force)
+			const (fun glb force -> Global.run ~env: eio_env glb @@ run force)
 			$ Global.args
 			$ force_arg
 			$ names_arg
@@ -315,8 +320,9 @@ module List_stale = struct
 
 	let term ~env =
 		let open Cmdliner in
+		let eio_env = env in
 		Term.(
-			const (fun glb -> Global.run ~env glb @@ run)
+			const (fun glb -> Global.run ~env: eio_env glb @@ run)
 			$ Global.args
 		)
 
@@ -345,11 +351,73 @@ module Refresh = struct
 				& info [] ~docv: "INPUT_NAME" ~doc: "Input names to refresh."
 			)
 		in
+		let eio_env = env in
 		Term.(
-			const (fun glb -> Global.run ~env glb @@ run)
+			const (fun glb -> Global.run ~env: eio_env glb @@ run)
 			$ Global.args
 			$ names_arg
 		)
 
 	let cmd ~env = Cmdliner.Cmd.v info (term ~env)
 end
+
+module Upgrade = struct
+	let info =
+		Cmdliner.Cmd.info
+			"upgrade"
+			~doc: "Upgrade lockfile & manifest to current schema version."
+			~exits: Cmdliner.Cmd.Exit.defaults
+			~man: common_man
+
+	let run ~env: _ ~domain_count: _ from to_ dry_run : unit =
+		let open Nixtamal in
+		match upgrade ?from ?to_ ~dry_run () with
+		| Ok () -> ()
+		| Error err -> failwith (Fmt.str "%a" Nixtamal.Error.pp err)
+
+	let term ~env =
+		let eio_env = env in
+		let open Cmdliner in
+		let version_conv : Nixtamal.Schema.Version.t Arg.conv =
+			Arg.conv
+				~docv: "VERSION"
+				((fun s ->
+					match Nixtamal.Schema.Version.of_string s with
+					| Some v -> Ok v
+					| None ->
+						let valid = Fmt.(array ~sep: comma Nixtamal.Schema.Version.pp) in
+						Error (`Msg (Fmt.str "Invalid version %s. Valid versions: %a" s valid Nixtamal.Schema.Version.versions))
+				),
+				 Nixtamal.Schema.Version.pp)
+		in
+		let from_arg =
+			let doc = "Upgrade from a specific version. Must match the lockfile version." in
+			Arg.(
+				value
+				& opt (some version_conv) None
+				& info ["from"] ~doc ~docv: "VERSION"
+			)
+		and to_arg =
+			let doc = "Upgrade to a specific version. Must be newer than --from." in
+			Arg.(
+				value
+				& opt (some version_conv) None
+				& info ["to"] ~doc ~docv: "VERSION"
+			)
+		and dry_run_arg =
+			Arg.(
+				value
+				& flag
+				& info ["dry-run"] ~doc: "Show what would be upgraded without making changes."
+			)
+		in
+		Term.(
+			const (fun glb -> Global.run ~env: eio_env glb @@ run)
+			$ Global.args
+			$ from_arg
+			$ to_arg
+			$ dry_run_arg
+		)
+
+	let cmd ~env = Cmdliner.Cmd.v info (term ~env)
+end
diff --git a/bin/dune b/bin/dune
index 5705f13..f36fcea 100644
--- a/bin/dune
+++ b/bin/dune
@@ -13,6 +13,7 @@
   logs.cli
   logs.fmt
   uri)
+ (flags (:standard -alert -deprecated))
  (preprocess
   (pps ppx_deriving.show ppx_deriving.eq ppx_deriving.ord ppx_deriving.make)))
 
diff --git a/bin/main.ml b/bin/main.ml
index bdb25e7..739776f 100644
--- a/bin/main.ml
+++ b/bin/main.ml
@@ -27,6 +27,7 @@ let cmd ~env =
 		Cmd.Lock.cmd ~env;
 		Cmd.List_stale.cmd ~env;
 		Cmd.Refresh.cmd ~env;
+		Cmd.Upgrade.cmd ~env;
 	]
 	in
 	Cmdliner.Cmd.group info subcommands