In case more is needed

local moduleManip = peripheral.wrap("top") -- Fix this
if moduleManip ~= nil then
	moduleManip.capture("^!")
end
local mName = "&h(bagel 'n roger wuz here.)&i(https://www.youtube.com/watch?v=ByC8sRdL-Ro)<&r&dAllium&r>" --bot title

local color = require("color") --Sponsored by roger109z
local allium = {} -- API table
local plugins = {} -- Plugin table

allium.assert = function(condition, message, level)
	if not condition then error(message, level) end
end

allium.register = function(name)
	assert(type(name) == "string", "Invalid argument #1 (string expected, got "..type(name)..")", 2)
	assert(plugins[name:lower()] == nil, "Invalid argument #1 (plugin exists under name "..name:lower()..")")
	plugins[name:lower()] = {threads = {}, commands = {}, info = {}, name = name}
	local funcs = {}
	local this = plugins[name:lower()]
	funcs.command = function(name, command, info)
		assert(type(name) == "string", "Invalid argument #1 (string expected, got "..type(name)..")", 2)
		assert(type(command) == "function", "Invalid argument #2 (function expected, got "..type(command)..")", 2)
		assert(this.commands[name:lower()] == nil, "Invalid argument #2 (command exists under name "..name:lower().." for plugin "..this.name..")", 2)
		assert(type(info) == "string", "Invalid argument #3 (string expected, got "..type(info)..")", 2)
		this.commands[name:lower()] = command
		this.info[name:lower()] = info
	end

	funcs.thread = function(thread)
		assert(type(thread) == "function", "Invalid argument #1 (function expected, got "..type(thread)..")", 2)
		this.threads[#this.threads+1] = thread
	end
	return funcs
end

allium.tell = function(name, message, hidetag, botname) --allium.tell as documented in README
    local m
    if type(message) == "string" then
        m = message
    else
        m = ""
    end
    if type(botname) ~= "string" then
    	botname = mName
    end
    local _, test = commands.tellraw(name, color.format((function(hidetag)if hidetag then return "" else return botname.."&r " end end)(hidetag)..m))
    if type(message) == "table" then
        for k, v in pairs(message) do
            local _, l = commands.tellraw(name, color.format(v))
        end
    end
    return textutils.serialise(test)
end

allium.getPlayers = function()
	local didexec, input = commands.exec("list")
	if not didexec then
		local _, users = commands.testfor("@a")
		local out = {}
		for i = 1, #users do
			out[#out+1] = string.sub(users[i], 7, -1)
		end
		return out
	end
	local out = {}
	for user in string.gmatch(input[2], "%S+") do
		local comma = string.find(user, ",")
		if not comma then comma = -1 else comma=comma-1 end
		out[#out+1] = string.sub(user, 0, comma)
	end
	return out
end

allium.getPersistence = function(name) --allium.getPersistence as documented in README
	if fs.exists("persistence.json") then
		local fper = fs.open("persistence.json", "r")
		local tpersist = textutils.unserialize(fper.readAll())
		fper.close()
		if not tpersist[origin] then
			tpersist[origin] = {}
		end
		if type(name) == "string" then
			return tpersist[origin][name]
		end
	end
	return false
end

allium.setPersistence = function(name, data) --allium.setPersistence as documented in README
	local tpersist
	if fs.exists("persistence.json") then
		local fper = fs.open("persistence.json", "r")
		tpersist = textutils.unserialize(fper.readAll())
		fper.close()
	end
	if not tpersist[origin] then
		tpersist[origin] = {}
	end
	if type(name) == "string" then
		tpersist[origin][name] = data
		local fpers = fs.open("persistence.json", "w")
		fpers.write(textutils.serialise(tpersist))
		fpers.close()
		return true
	end
	return false
end

allium.getInfo = function(plugin, command) -- Get the information of all plugins, a single plugin, or a single command from a plugin
	assert(plugin == nil or type(plugin) == "string", "Invalid argument #1 (string expected, got"..type(plugin)..")", 2)
	assert(command == nil or type(command) == "string", "Invalid argument #2 (string expected, got"..type(command)..")", 2)
	if command then
		assert(plugin, "Invalid argument #1 (string expected, got"..type(plugin)..")", 2)
	end
	if plugin then
		assert(plugins[plugin], "Invalid argument #1 (plugin "..plugin.." does not exist)", 2)
		if command then
			assert(plugins[plugin].command[command], "Invalid argument #2 (command "..command.." does not exist in plugin "..plugin..")")
		end
	end
	if command then
		return plugins[plugin].info[command]
	elseif plugin then
		local res = {}
		for k, v in pairs(plugins[plugin].info) do
			res[k] = v
		end
		return res
	else
		local res = {}
		for p_name, plugin in pairs(plugins) do
			res[p_name] = {}
			for c_name, info in pairs(plugin.info) do
				res[p_name][c_name] = info
			end
		end
		return res
	end
end

local function is_require() -- This function was elegantly made by SquidDev
	-- See: https://discordapp.com/channels/477910221872824320/477911902152949771/536123240154660864
	if not shell then return("os.loadAPI") end
	if not package then return "shell.run" end -- Compat for old versions of CC

	-- Locate the sentinel value, and check that it's currently within the table
	-- somewhere.
	package.preload["__sentinel"] = function() return package.loaded["__sentinel"] end
	local sentinel = require("__sentinel")
	for k, v in pairs(package.loaded) do
		if k ~= "__sentinel" and v == sentinel then return "require" end
	end

	return "shell.run"
end
package.loaded["__sentinel"] = nil
local is_it = is_require()

if is_it == "require" then
	return allium
elseif is_it == "os.loadAPI" then -- Please for the love of god never use os.loadAPI
	_G.allium = allium
end

do -- Plugin loading process
	print("Loading plugins...")
	local dir = shell.dir()
	if fs.exists(dir.."plugins") then
		for _, plugin in pairs(fs.list(dir.."plugins")) do
			if not fs.isDir(dir.."plugins/"..plugin) then
				local file = loadfile(dir.."plugins/"..plugin)
				local suc, err = pcall(file)
				if not suc then
					printError(err)
				end
			end
		end
	end
end


local main = function()
	while true do
		local _, message, _, name = os.pullEvent("chat_capture") --Pull chat messages
		if string.find(message, "!") == 1 then --are they for allium?
			args = {}
			for k in string.gmatch(message, "%S+") do --put all arguments spaced out into a table
				args[#args+1] = k
			end
			local cmd = args[1]:sub(2, -1) -- Strip the !
			table.remove(args, 1) --remove the first parameter given (!command)
			local p_cmds = {} -- List of possible commands if there's more than one that matches the "!command" standard
			if not string.find(cmd, ":") then --did they not specify the plugin source?
				print(#plugins)
				for p_name, plugin in pairs(plugins) do --nope... gonna have to find it for them.
					print(p_name)
					for c_name, command in pairs(plugin) do
						print(c_name)
						if c_name == cmd then --well I found it, but there may be more...
							p_cmds[#p_cmds+1] = {command, p_name} --split into command function, source
						end
					end
				end
			else --hey they did! +1 karma.
				local splitat = string.find(cmd, ":")
				if plugins[string.sub(cmd, 1, splitat-1)] then --check plugin existence
					if plugins[string.sub(cmd, 1, splitat-1)].commands[string.sub(cmd, splitat+1, -1)] then --check command existence
						p_cmds[#p_cmds+1] = {plugins[string.sub(cmd, 1, splitat-1)].commands[string.sub(cmd, splitat+1, -1)], string.sub(cmd, 1, splitat-1)} --split it into the function, and then the source
					end
				end
			end
			if #p_cmds == 1 and p_cmds[1][1] then --is it really a command, and is there only one that is titled this?
	    		local stat, err = pcall(p_cmds[1][1], name, args) --Let's execute the command in a safe environment that won't kill allium
	    		if stat == false then--it crashed...
	    			allium.tell(name, "&4"..cmd.." crashed! This is likely not your fault, but the developer's. Please contact the developer of &a"..p_cmds[1][2].."&4. Error:\n&c"..err)
	    			print(cmd.." errored. Error:\n"..err)
	    		end
	    	elseif #p_cmds > 1 then --WHAT MORE THAN ONE OUTCOME!?!?
	    		local colstr = ""
	    		for i = 1, #p_cmds do --idiot, I'm going to have to list them out for you...
	    			if i ~= #p_cmds then
	    				colstr = colstr.."&a&g(!"..p_cmds[i][2]..":"..cmd..")&h(Click to run !"..p_cmds[i][2]..":"..cmd..")"..p_cmds[i][2].."&r&e, "
	    			else
	    				colstr = colstr.."and &a&g(!"..p_cmds[i][2]..":"..cmd..")&h(Click to run !"..p_cmds[i][2]..":"..cmd..")"..p_cmds[i][2].."&r&e."
	    			end
	    		end --how dare you inconvenience me...
	    		allium.tell(name, "&eCommand collision beween "..colstr.." Click on the plugin that you want to run the command from. Optionally specify the command you want to use by prefixxing the plugin name followed by a colon, and then the command name. Ex: &c&g(!allium:github)!allium:github&r&e.") --REEEEEEEE
    		else --this isn't even a valid command...
	    		allium.tell(name, "&6Invalid Command, use &c&g(!allium:help)!help&r&6 for assistance.") --bleh!
    		end
	    end
	end
end

local threads = {} -- Temporary

threads[#threads+1] = coroutine.create(main) --Add main to the thread table

if not fs.exists("persistence.json") then --In the situation that this is a first installation, let's add persistence.json
	local fpers = fs.open("persistence.json", "w")
	fpers.write("{}")
	fpers.close()
end

print("allium started.")
allium.tell("@a", "allium loaded.")
--This clump is pulled and adapted for what I need it for, parallel.waitForAll, for a table of coroutines. Its origin is in /rom/apis/parallel.lua in CraftOS.
local count = #threads
local living = count

local tFilters = {}
local eventData = { n = 0 }
while true do
	for n=1,count do
		local r = threads[n]
		if r then
			if tFilters[r] == nil or tFilters[r] == eventData[1] or eventData[1] == "terminate" then
    			local ok, param = coroutine.resume( r, table.unpack( eventData, 1, eventData.n ) )
				if not ok then
					error( param, 0 )
				else
					tFilters[r] = param
				end
				if coroutine.status( r ) == "dead" then
					threads[n] = nil
					living = living - 1
					if living <= 0 then
						return n
					end
				end
			end
		end
	end
	for n=1,count do
		local r = threads[n]
		if r and coroutine.status( r ) == "dead" then
			threads[n] = nil
			living = living - 1
			if living <= 0 then
				return n
			end
		end
	end
	eventData = table.pack( os.pullEventRaw() )
end