The "good in the flesh" is referring to Saul's disobedience. Saul was instructed to defeat and destroy Amalek. Saul succeeded in defeating Amalek but didn't destroy everything. Saul kept the best of the spoils to offer to God. He thought he was doing good, but was not doing God's will. Ian Thomas is referring to 1 Sam 15 and even mentions the chapter just before the part you have quoted.
The character of Saul is a far cry from that I was describing in my questions.
It doesn't appear to me that Ian Thomas viewed the Christian's works as filthy rags. Just a few paragraphs before the single sentence you quoted:
As far as God is concerned, Christ is the preacher, Christ is the missionary, Christ is the Christian worker, Christ is the witnessing Christian. Only what He is and what He does is righteousness - and what He is and what He does is released through you only by your unrelenting attitude of dependence. This is called faith - and "whatsoever isn't of faith is sin"(Rom 14:23c)
It is a shock to discover that you can go up into the pulpit with a Bible in your hand, preach a sermon entirely scriptural in its content, and yet if this be done in anything other than an attitude of total dependence upon Christ, in the very act of preaching you are committing sin.
This is not milk for babies but meat for the strong, who are "of full age", but "hard to be uttered"(Heb 5:11), for we have become accustomed to the elaborate machinery of the church, as an organizational enterprise in which carnal activity on the part of Christians is not only tolerated, but solicited- often in sublime sincerity and with a false sense of dedication on the part of those involved, who, being ignorant of the "very first principles of God's Word," are "unskilled in the doctrine of righteousness." -Ian Thomas, The Saving Life of Christ
It appears to me, from the underlined portions in his writing, that works done as a result of dependence on God are not viewed as "filthy rags" by Ian Thomas.
Care to address the questions I asked LuarenTM?
Here's another of the Thomas's quote that clarifies much....
"You may have harnessed the energy of the flesh in an otherwise quite genuine desire to honor the Lord Jesus in your life. The flesh, which has its origin in Satan, will go along with you; to survive, it is quite prepared to engage in every form of Christian activity, even though this may seem to honor Christ.
The flesh will sing in the choir, teach Sunday school, preside at a deacons’ meeting, preach from the pulpit, organize an evangelistic crusade, go to Bible college, volunteer for the mission field, and a thousand other things, all of which may in themselves be otherwise legitimate, if only it can keep its neck out of the noose. The flesh will threaten, shout, strut, domineer, sulk, plot, creep, beg, pleased, or sob, whatever the situation may demand in the interests of its own survival. By any and all means it will seek to cause every Christian to live by his own strength instead of by the power and grace of the Lord Jesus, and to conclude that doing so is actually a good thing!
The characteristic of the spiritually immature is that they are unable to discern between good and evil (Hebrews 5:13-14), and the baby Christian, like the foolish Galatians, “having begun in the Spirit” still tries to be “made perfect by the flesh” (Galatians 3:3).
We must be particularly patient with those whose lack of understanding allows a genuine love for the Lord Jesus to be satisfied with, and sometimes to be quite enthusiastic about, Christian activities involving means and methods which are heavily contaminated by the flesh. These are more deserving of instruction than rebuke, for they are still in their spiritual babyhood.
True spiritual conviction is an activity of the Holy Spirit within the human spirit, and when the Holy Spirit begins to convict you of your immaturity, bearing witness to your conscience that the Lord Jesus Christ is being denied His rightful place in your life, the old Adam-nature within you becomes irritable and edgy. At the same time it will seek to produce the most plausible arguments in justification of its own illegitimate activities, even though these activities are only what the Bible calls “dead works” (Hebrews 6:1; 9:14) and not the “good works” which are truly the work of God.
“Good works” are those that have their origin in Jesus Christ, as Christ’s activity is released through your body because you present it to Him as a living sacrifice. You do this only by faith that expresses total dependence, as opposed to Adamic independence."