Let's address the elephant in the room first. LuaRocks is indented with 3 spaces.
for i, pkg in ipairs(packages) do
   for name, version in pairs(pkg) do
      if name == searched then
         print(version)
      end
   end
end
Rationale: There is no agreement in the Lua community as for indentation, so 3 spaces lies nicely as a middle ground between the 2-space camp and the 4-space camp. Also, for a language that nests with do/end blocks, it produces pleasant-looking block-closing staircases, as in the example above.
One should not use tabs for indentation, or mix it with spaces.

Use LF (Unix) line endings.

Document function signatures using LDoc. Specifying typing information after each parameter or return value is a nice plus.
--- Load a local or remote manifest describing a repository.
-- All functions that use manifest tables assume they were obtained
-- through either this function or load_local_manifest.
-- @param repo_url string: URL or pathname for the repository.
-- @param lua_version string: Lua version in "5.x" format, defaults to installed version.
-- @return table or (nil, string, [string]): A table representing the manifest,
-- or nil followed by an error message and an optional error code.
function manif.load_manifest(repo_url, lua_version)
   -- code
end
Use TODO and FIXME tags in comments. TODO indicates a missing feature to be implemented later. FIXME indicates a problem in the existing code (inefficient implementation, bug, unnecessary code, etc).
-- TODO: implement method
local function something()
  -- FIXME: check conditions
end
Prefer LDoc comments over the function that explain what the function does than inline comments inside the function that explain how it does it. Ideally, the implementation should be simple enough so that comments aren't needed. If the function grows complex, split it into multiple functions so that their names explain what each part does.