Historical Developments that led to the eclipsing of the doctrine of Justification by Faith alone

James Swan had linked to this book on Purgatory and I recently received it in the mail and it is really interesting and helpful in getting a handle on how this unbiblical doctrine developed in church history.
(see under point 5)

The biblical doctrine of justification by faith alone was eventually neglected, over-shadowed, and eclipsed by the slow development of other unbiblical doctrines and doctrines.

It (Justification by grace through faith alone) appears at times in the writings of early Christians and early church fathers; but because some of these others things (listed below) were also developing at the same time, and sometimes some early church writers were inconsistent in seeming to affirm the doctrine of justification by faith alone, and also some of the other things listed below; this is one of the great reasons for why it is so hard and complicated to figure out what the early church believed about the doctrine after the Biblical era, and until Wycliffe, Hus, and Luther questioned these things.

1.  The Mono-Episcopate:  Biblical elders of a plurality of leaders was changed into taking one of the gifted elders out of the college and making him the sole bishop over the other elders in a church; then, later, in an entire area/city.  We can see that elders and bishops were interchangeable in the NT and in the earliest extra-canonical writing 1 Clement (96 AD), the Didache, Shepherd of Hermas.  Then, later we see a change in Ignatius (107-117 AD) and then Cyprian (around 250 AD) takes it further, and beyond in history.  see here for an Evangelical Introduction to church history part 1; and then, Part 2 here, that fleshes it all out.   But even Ignatius knows he does not have authority like an apostle.  (see his epistle to the Magnesians, epistle to the Trallians paragraph 3, verse 3, Ignatius to the Romans, paragraph 4, verse 3, and Ignatius to the Ephesians, paragraph 3, verse 1.  See also here, John Bugay has many excellent articles on this issue here and at Triablogue.   Even Cyprian, though he championed the ideas of the mono-episcopate of a local area, and that "the bishop is the church"; even he, did not agree that the bishop in Rome was the bishop of bishops.  He and 86 other bishops from all over the Christian world at the time, clearly stood against Stephen, the bishop of Rome at the time, in 258 AD.   Much later, the jurisdiction of the bishop of Rome seems to have taken off some by Leo 1 in 440 AD, and then even more from Gregory the Great in 601 AD onward.  After Gregory the Great the power of the bishop of Rome kept developing, reaching a high mark of arrogance and false doctrine in Boniface VIII's statement in 1302 in the document, Unam Sanctum, ("It is necessary for every human creature to be in submission to the Roman Pontiff for salvation."); to the arrogance of Pius IX with "I am the tradition"; thus eventually developed into the Papal doctrines and dogma of infallibility in 1870.

2.  Baptismal Regeneration:  NT baptism as an outward evidence and sign/symbol of repentance and faith, an inward reality of regeneration/being born again/union with Christ by faith and repentance was changed into having power to actually cause one to be born again and regenerated. (baptismal regeneration)  The debate and discussion on that issue is still going strong in the com boxes here. 

3.  Penance:  Internal Repentance in the NT was changed into an outward penance, the work of satisfaction that one was assigned to do by a priest after confession.  William Webster has an excellent article on this the combines a lot of the other points also.    This was the first point of protest by Martin Luther in his 95 theses.  Later penance was developed along with private confession to a priest along with purgatory and then, with the treasury of merit of the saints into indulgences which really "took off" during the Crusades and was the spark that started Martin Luther questioning the Roman Catholic Church in 1517.

Addendum:  (January 3, 2014) - John Bugay made an excellent addition in the com box (on Aug. 15, 2012) to this issue on how the Latin mis-translation of the Greek word for repentance affected subsequent theology and church history. 

4.  Private Confession of sins to the priest for forgiveness:  Biblical confession of sin (1 John 1:9; James 5:16), and public confession of serious sin, developed into private confession of sins to a priest.  See also William Webster's article under point # 3.  Later, ex opere operato powers were given to the priests after the Donatist controversy.

5.  Purgatory - The idea of some kind of after death purging and cleansing was developed into Purgatory, starting with Clement of Alexandria and Origen and developing more after Augustine, especially by Gregory the bishop of Rome in 601 AD. See -
The Birth of Purgatory, by Jacques Le Goff. 

 James Swan has earlier linked to an excellent book called The Birth of Purgatory by Jacques Le Goff.   (Scroll down in this "Resources on Roman Catholicism" blog article)

6.  A NT office of priests.  This was wrong, as there is no NT office of "priest" in the local church.  None.  Jesus is our high priest.  For the NT church, there are
a. elders/overseers (same as bishops)/pastors and b.  deacons.  Every believer/saint is a priest to God.  (1 Peter 2:5-10; Revelation 1:6; 5:9-10.)   The word "priest" seems to be first applied to elders and ministers after they started applying OT language of sacrifice in worship to the thanksgiving and worship in the church and at the celebration of the eucharist.  (see # 13)

7.  Categories of mortal sins and venial sins and distinguishing between them. That seems to have started with Tertullian.

8.  Ideas of merit for good works, which is a contradiction to the Biblical teachings on grace.

9.  Gaining merit through Pilgrimages to graves and holy sites.  Simple remembering of martyrs' day of death as a "birthday" (going to heaven) and then venerating their bones (Would Polycarp have approved of such a practice?) , then to pilgrimages and visiting graves of dead saints and praying to them at their graves.

10.  Prayers to dead saints.  Whether at their graves or later, in front of pictures, later the icons, or statues.

11.  Prayers to Mary and the over-exalting of Mary as the greatest mediator, and then later other false dogmas such as Mary's Perpetual Virginity, her sinlessness, her Immaculate Conception(1854), and the Bodily Assumption (1950).  She is called, "co-mediatrix" - a clear contradiction to 1 Timothy 2:5.

12.  Almsgiving as a way of satisfaction for sins, often part of the penance assigned by a priest.

13.  Sacrificial language of the mass.  From using NT language of the sacrifices at the temple (Matthew 5:23-26), combining it with the need to reconcile with brothers before worship (Matthew 18:15-20) and taking the sacrificial language of the prophesy of Malachi 1:11 and applying all of that to the eucharist/Lord's supper in 1 Corinthians 11/Luke 22/Matthew 26. The sacrificial language of the OT (Malachi) and NT (Matthew 5:23-26) was not meant to say that the eucharist would be a sacrifice, but rather an application of OT language to worship/thanksgiving/memorial of Christ's death/celebration in the NT church.

14.   Transubstantiation:  From memorial/spiritual presence of Christ in communion/ eucharist (Biblical) to actual physical presence (Justin Martyr to Radbertus in the 800s) to transubstantiation (developed from the 800s into 1215 AD)

Sometimes the doctrine of justification by faith alone can be discerned in the early church, in the writings of Clement, The Epistle to Diognetes, and Ambrosiaster seem to be really clear references.  Also, later, in the writings of John Chrysostom seems clear, and in others, but they sometimes had some elements of the above practices and doctrines also.  So they were inconsistent.  These 14 practices/doctrines together (and probably with other issues not named here, too) combined to eclipse / hide the doctrine of justification by faith alone, like the moon hiding the sun in an eclipse.   All of these things combined together to over-shadow the doctrine of justification by faith alone over the centuries until Wycliff and Hus and Luther started questioning these things.