Some more snippets

Sir Thomas had a rivalry with Richard Masterson in the late 16th and early 17th century. Richard Masterson  held a number of crown offices which irked Sir Thomas, Masterson had been in Wexford for a much shorter time than Colclough. But Sir Thomas had been overlooked for offices such  the senechal.
However during the rebellion or nine years war which began in 1596 the area of N. Wexford known as Scarawalsh saw a member of the Kavanagh clan Donal Spainneach among the first to take up arms, an account at the time told how '...Hovenden an Englishman but a papistical traitor took Donal's son and carried him to the earl of Tyrone, with the consent of his father as a pledge of his fidelity to the earl...' The earl being the O'Neill who was captured off the coast of Lough Swilly Co. Donegal see one of my earlier posts.
Anyway the reason for this preamble is that although the Irish and those Anglo-Irish that supported them (not Colclough's) were quite unsuccessful in their rebellion, they had a notable victory on 19th May 1598 when they fought crown forces. Forces which were assembled by Sir Thomas suspending his rivalry with Masterson, and forming a group of 400 soldiers to fight the Kavanagh's, Sir Thomas and Masterson lost 309 men among them Leonard Colclough brother of Sir Thomas... Leonard was High Sheriff of Wexford in 1596 he resided at Ballyknockan, Queens County nowadays Co Laois, he was married to Honora Walsh daughter of Walter Walsh 'Lord of the mountains' of Co Kilkenny.

This area of N. Wexford became the subject of a 'plantation' between 1620 and 1640, interesting again with my Co. Donegal Ulster ancestry.
Because the above Masterson was still senechal of the area he was responsible for land allocation that is taking it from the Irish and giving it to English or Welsh (unlike the Scottish of the north) and the rivalry, discord and jealousies had restarted after the brief truce. Sir Thomas was not a beneficiary of plantation he did however build up large estates in N. Wexford by purchase, mortgaging and mortgage foreclosure to local Irish.

In 1628 these lands passed to Dudley Colclough he was the eldest son of Sir Thomas and Elinor Bagenal, he suceeded to the Duffry from his father's will, his half brother Sir Adam having Tintern. He took possession of the Scarawalsh lands in 1624 when he was 15 years old, he was living then at Monart in the Duffry. He married Katherine Esmonde who was the daughter of Patrick Esmonde of the house of Johntown in N. Wexford, Katherine was one of 3 Patrick's 3 co-heirs Dudley obtained more land in N. Wexford from this marriage. He also used purchases and mortgage foreclosures, and his second marriage to Mary daughter of Sir Patrick Barnewall of Brickstown he amassed 11,885 acres in N.Wexford making him the biggest land holding in that barony of Scarawalsh.

Dudley sided with Confederate Ireland a period of Irish self-government between 1642 and 1649, During this time, about 60% of Ireland was governed by the Irish Catholic Confederation, also known as the "Confederation of Kilkenny". This was formed by Irish Catholic nobles, clergy and military leaders after the rebellion of 1641.

The Confederation had a General Assembly, a Supreme Council, and a Military. It pledged allegiance to Charles 1. Throughout its existence, the Confederation waged war against the parliamentarians. In 1648, it allied itself with the royalists. However, in 1649 a parliamentarian army under Cromwell invaded Ireland, it defeated the Confederates and Royalists and brought the Confederation to an end.

This is relevant to the Colclough family because they were on different sides a theme to follow us through:

Adam the eldest son of Sir Thomas was created a baronet in 1628, then became Sir Adam, he married Alice daughter of Robert Rich , Master in Chancery in England, their only son Caesar who became Sir Caesar on succession to his father in 1637. His home Tintern was garrisoned by a small force of 30 parliamentarian soldiers from Duncannon during the 1641 rebellion. Dudley and his 2 brothers Anthony and John who were with the confederates were offered £400 to take Tintern, but while Lady Alice (their 'half' sister-in-law) was in residence they did not besiege the stronghold, however when she left Tintern in the spring of 1642 they took it.

When the rebellion was suppressed Dudley and his brothers were meant to be stripped of their lands and transplanted to Connaught but legal appeals, side switching and religion changing meant this never really happened. But was most probably was due to negotiations behind the scenes using marriage connections. While the Cromwell period was underway Dudley went to live at Huntingdon Castle in Clonegal Co. Carlow, this had been built by Katherine Esmonde's uncle who was Lord Esmonde. Dudley died in 1663, his family probably stayed there until 1674 when it is likely that they moved back to Duffry Hall...
Below are a couple of maps showing landholdings in Wexford:
                         

Wexford landowners 1640

Wexford landowners 1705

Much of the above information is sourced from books I have including the Colclough papers, The Wexford Gentry Volume 1 Art Kavanagh and Rory Murphy, and Wexford History and Society Ed. Kevin Whelan.