lua metaprogram: Delete dead code, some more lifting to duffle

scripts/passes/annotation.lua

@@ -18,10 +18,10 @@
 -- Bootstrap: load `scripts/duffle_paths.lua` (sets package.path + package.cpath).
 -- Uses `debug.getinfo` to find this file's own directory, so it works
 -- both standalone and when require'd from the orchestrator.
-local _src = debug.getinfo(1, "S").source:sub(2)
-local _dir = _src:match("(.*[/\\])") or "./"
-dofile(_dir .. "../duffle_paths.lua")
-local duffle = require("duffle")
+-- Bootstrap: load `duffle_paths.lua` via `debug.getinfo(1, "S").source` (works both standalone + when require'd).
+-- duffle_paths.lua sets package.path then returns `require("duffle")` at the bottom, so the dofile value IS the duffle module.
+local _bootstrap_dir = debug.getinfo(1, "S").source:match("^@?(.*[/\\])") or "./"
+local duffle        = dofile(_bootstrap_dir .. "../duffle_paths.lua")
 local write_file          = duffle.write_file
 local ensure_dir          = duffle.ensure_dir
 
@@ -329,11 +329,7 @@ function M.run(ctx)
 
 	-- Per-DIRECTORY (per-module) aggregation. Group sources by `src.dir`,
 	-- validate every source in the dir, then emit ONE errors.h per dir.
-	local by_dir = {}
-	for _, src in ipairs(ctx.sources) do
-		by_dir[src.dir] = by_dir[src.dir] or {}
-		table.insert(by_dir[src.dir], src)
-	end
+	local by_dir = duffle.group_sources_by_dir(ctx.sources)
 
 	for dir, dir_sources in pairs(by_dir) do
 		local dir_basename = dir:match("([^/\\]+)$") or dir