The answer to this question begins with a book. In the summer of 1957, pro-independence journalist Henri Alleg, a European Jew living in French Algeria, was arrested and tortured by paratroopers under the command of General Jacques Massu in Algiers. A year later, Alleg's book La Question (The Question) is released. While imprisoned, Alleg not only wrote the manuscript but also smuggled it out of prison with the help of his lawyer. In the book, Alleg gives an intimate and detailed chronicle of his torture at the hands of French soldiers at the El-Biar detention center. Within two weeks, the book had sold 60,000 copies. Within yet another month, the French government banned the book. Despite this, the book caused great controversy in Metropolitan France and abroad. The French government officially denied the allegations put forward by Alleg, but the question had picked up pace amongst the broader public who called for further investigations.

The publication of La Question in early 1958 was the climax of questions and revelations that had occured throughout 1957. Strict censorship had prevented journalists in Algeria to spread the word about torture, but this could not last forever. Starting in 1955, allegations of torture were published in French newspapers. These allegations, as well as allegations by the FLN, gave French prime minister Guy Mollet no choice but to form the Commission de sauvegarde des droits et libertés individuels (Commission to Safeguard Individual Rights and Liberties) in 1957 to investigate the matter. Although the commission would ultimately find its investigation tbe restricted by the French government, with visits to facilities either restricted or overseen by the French army, the commission did conclusively find the presence of torture (but, they claimed, not in a systematic way). In December 1957, two months before the publication of La Question, Le Monde leaked the commission's conclusions. The set was stage for La Question.

The topic of torture, therefore, became very widespread in 1958. The FNL actively used it as a tool for their own propaganda while the French government claimed that the allegations were untrue, even going so far as to publish a report in 1960 in which the FLN reports were claimed to be fabricated and that marks of tortures were actually self-inflicted. In the more public sphere, torture in Algeria was likened to torture in occupied France during the Second World War by German soldiers. After these revelations, France could never represent itself as a beacon of 'Western civilization' in opposition to the 'Algerian barbarians'. Despite its accomplished military performance during the war, France ultimately lost the war because it lacked any credibility amongst the Algerian people. The widespread atrocities helped France lose the war.

After 1962, the matter didn't go away. It was repeatedly brought up. The main difference here, however, is that torture was considered by some as either justified or non-systematic. General Jacques Massu answered in the affirmative upon asked after the war whether or not there was torture during the war, stating that "it was never either institutionalised or codified... I am not frightened of the word." Additionally, in 1970 upon meeting Alleg, Massu stated to the press that "Do the torments which he suffered count for much alongside the cutting off of the nose or of the lips, when it was not the penis, which had become the ritual present of the fellaghas to their recalcitrant 'brothers'? Everyone knows that these bodily appendages don't grow again!". Massu's justification was common among French army officers who had participated in the torture. Soldiers like Colonel Roger Trinquier would repeatedly justify torture by claiming that it was the only way to win the war. Torture was therefore not unknown to the French general public. As William B. Cohen points out, polls in 1979 and 1987 all showed that more than 59 % and 67 % respectively were aware and acknowledged that torture had taken place during the Algerian War.

Despite this public awareness, the topic did not attract too much scholarly attention. . In fact, as you point out, there wasn't much research made until the 1990s because of controversies, such as the 1997-1998 trial of Maurice Papon. Maurice Papon had collaborated with Nazi Germany during the Second World War and in the post-war years, served as an administrator in both Morocco and Algeria as well as having been the Prefect of Police for Paris during the 1961 Paris massacre in which Parisian policemen attacked and killed hundreds of Algerians during a protest against the war. The links between the Second World War and the Algerian War were now laid open for the public, just as it had been in the late 1950s. With the opening of the archives in the late 90s, new evidence was brought forward. In the early 2000s, interviews with Massu and General Marcel Bigeard about the atrocities during the war was published in the pages of Le Monde and reached its climax with the publication of General Paul Aussaresses' Services spéciaux, Algérie 1955-1957: Mon témoignage sur la torture (2001). Like Massu and Bigeard, Aussaresses had been interviewed by Le Monde and had likewise defended torture using the same arguments.

What made the 2018 acknowledgements by Emmanuel Macron so ground breaking? In comparison to past acknowledgement of torture, the fact that Macron focused on the systematic usage of torture, instead of it being sporadic as generals and officers had claimed in the past, meant that a more full understanding and acknowledgement of the realities of torture during the Algerian War was finally reached. It also brought closure to the case of Maurice Audin; he had been a friend of Henri Alleg and had been arrested one day before Alleg was arrested. Alleg would ultimately escape his prison and live out his life, dying in 2013. Audin was tortured to death, perhaps by the same soldiers who had tortured Alleg.

Sources:

Algeria: France's Undeclared War by Martin Evans (Oxford University Press, 2012)

A Savage War of Peace - Algeria 1954-1962 by Alistair Horne (Macmillan, 1977).

The Battle for Algeria: Sovereignty, Health Care, and Humanitarianism by Jennifer Johnson (University of Pennsylvania Press, 2015).

"The Sudden Memory of Torture: The Algerian War in French Discourse, 2000-2001", William B. Cohen, French Politics, Culture & Society, Vol. 19, No. 3, (Fall 2001), pp. 82-94.

"Torture in the Algerian War", Tzvetan Todorov and Arthur Denner, South Central Review, Vol. 24, No. 1, On Torture (Spring, 2007), pp. 18-26.