makeFlow.js

// input string
var originString = [
  "st->io",
  "io->cond",
  "cond(yes)->op1",
  "cond(no)->op2",
  "op1->sop1",
  "op2->sop2",
  "sop1->io1",
  "sop2->io2",
  "io1->e1",
  "io2->e2",
  "e1->e",
  "e(yes)->x1",
  "e(no)->x2",
  "e2(yes)->y1",
  "e2(no)->y2"
]

var first = []
var second = []
var result = []
var resultIndex = 0

var findMatch = function(a, e) {
  return a.indexOf(e)
}

var findConditionYes = function(a, e) {
  return a.indexOf(e + "(yes)")
}

var findConditionNo = function(a, e) {
  return a.indexOf(e + "(no)")
}

var getEmptyIndex = function(result) {
  for (var i = 0; ; i++) {
    if (result[i] === undefined) return i
  }
}

var calc = function(frist, second, index, resultIndex) {
  if (index === -1) return

  result[resultIndex] = result[resultIndex] || []
  if (result[resultIndex].length === 0 || result[resultIndex][result[resultIndex].length - 1] !== first[index]) {
    result[resultIndex].push(first[index])
  }
  result[resultIndex].push(second[index])
  // first.splice(index, 1)
  // second.splice(index, 1)

  var nextIndex = findMatch(first, result[resultIndex][result[resultIndex].length - 1])

  if (nextIndex !== -1) {
    calc(first, second, nextIndex, resultIndex)
  } else if (first.length !== 0) {
    var nextYesIndex = findConditionYes(first, result[resultIndex][result[resultIndex].length - 1])  
    calc(first, second, nextYesIndex, getEmptyIndex(result))

    var nextNoIndex = findConditionNo(first, result[resultIndex][result[resultIndex].length - 1])
    calc(first, second, nextNoIndex, getEmptyIndex(result))
  }

  return result[resultIndex].join("->")
}

originString.forEach(v => {
  var e = v.split("->")
  first.push(e[0])
  second.push(e[1])
})

calc(first, second, 0, 0)

result.forEach(v => {
  console.log(v.join("->"))
})

// output:
// st->io->cond
// cond(yes)->op1->sop1->io1->e1->e
// e(yes)->x1
// e(no)->x2
// cond(no)->op2->sop2->io2->e2
// e2(yes)->y1
// e2(no)->y2