Hammerspoon Click-Through Support

init.lua

-- Helper: Find window under mouse
local function windowUnderMouse()
    local mousePos = hs.mouse.absolutePosition()
    for _, win in ipairs(hs.window.orderedWindows()) do
        if win:isVisible() then
            local frame = win:frame()
            if mousePos.x >= frame.x and mousePos.x <= frame.x + frame.w and
               mousePos.y >= frame.y and mousePos.y <= frame.y + frame.h then
                return win
            end
        end
    end
    return nil
end

-- Log file setup
local logfilePath = os.getenv("HOME") .. "/hammerspoon_clickthrough.log"
local logfile = assert(io.open(logfilePath, "a"))
local function log(message, level)
    level = level or "INFO"
    local timestamp = os.date("%Y-%m-%d %H:%M:%S")
    logfile:write(string.format("%s [%s] %s\n", timestamp, level, message))
    logfile:flush()
end

-- Eventtap: Focus window under mouse and log click
clickLogger = hs.eventtap.new({hs.eventtap.event.types.leftMouseDown}, function(event)
    local win = windowUnderMouse()
    local frontmost = hs.window.frontmostWindow()
    if win then
        if win:id() ~= (frontmost and frontmost:id()) then
            win:focus()
            log("Focused window: " .. (win:title() or "Untitled"))
        else
            log("Clicked already-focused window: " .. (win:title() or "Untitled"))
        end
    else
        log("No window under mouse")
    end
    return false -- allow original click
end)

clickLogger:start()

-- Graceful shutdown
hs.shutdownCallback = function()
    log("Hammerspoon shutting down", "INFO")
    logfile:close()
end

this will sometimes make you click through and ignore right-click context menus when they display over an unfocused window

This modified Eventtap will detect if there's a context menu under the mouse and allow clicking entries

-- Eventtap: Focus window under mouse and log click
clickLogger = hs.eventtap.new({hs.eventtap.event.types.leftMouseDown}, function(event)
    local win = windowUnderMouse()
    local frontmost = hs.window.frontmostWindow()
    local ax = require("hs.axuielement")
    local mousePos = hs.mouse.getAbsolutePosition()
    local element = ax.systemElementAtPosition(mousePos)
    if element then
        local role = element:attributeValue("AXRole")
        if role == "AXMenu" or role == "AXMenuItem" then
        return false
    else
        if win then
            if win:id() ~= (frontmost and frontmost:id()) then
                win:focus()
                log("Focused window: " .. (win:title() or "Untitled"))
            else
                log("Clicked already-focused window: " .. (win:title() or "Untitled"))
            end
        end
    end
    else
        log("No window under mouse")
    end
    return false -- allow original click
end)

adding to autoclave73's code: This will prevent click through Dialogs (e.g. Hammerspoon's Preferences):

clickLogger = hs.eventtap.new({hs.eventtap.event.types.leftMouseDown}, function(event)
    local ax = require("hs.axuielement")
    local mousePos = hs.mouse.absolutePosition()
    local element = ax.systemElementAtPosition(mousePos)
    if element then
        local role = element:attributeValue("AXRole")
        log("role: " .. (role or "Untitled role"))
        if role == "AXMenu" or role == "AXMenuItem" then
            -- allow original click
            log("Skip on role: " .. role)
            return false
        else
            local frontmost = hs.window.frontmostWindow()
            -- log("Frontmost window title: " .. (frontmost:title() or "Untitled"))
            -- log("Frontmost window subrole: " .. (frontmost:subrole() or "not defined"))
            if nil ~= frontmost and frontmost:subrole() == "AXDialog" then
                -- allow original click
                log("Skip on subrole: " .. frontmost:subrole())
                return false
            else
                local win = windowUnderMouse()
                if win then
                    if win:id() ~= (frontmost and frontmost:id()) then
                        win:focus()
                        log("Focused window: " .. (win:title() or "Untitled"))
                    else
                        log("Clicked already-focused window: " .. (win:title() or "Untitled"))
                    end
                end
            end
        end
    else
        -- allow original click
        log("No window under mouse")
    end
    return false -- allow original click
end)