Indeed, Jonang tradition was banned and monasteries were closed at the
time of the Great Fifth Dalai Lama, Ngawang Lobsang Gyatso. But from
19th century AD onwards, Jonangpa order is freely to teach in the
public. Today in Tibet, there are more than 50 Jonangpa monasteries
throughout the country, supporting approximately 10,000 monks.

http://www.jonang.org/index.asp

Jetsun Taranatha's works were once banned during that period. However,
his works are once again studied in the Tibetan monasteries, such as the
one translated by Naropa University, "The Essence of Shentong", and his
other works, such as
"History Of Buddhism In India", "Golden Rosary" and many others, are
also studied in some monasteries and modern scholars.

So therefore, Jonang tradition IS a living tradition.

One may ask what did the Great Fifth Dalai Lama want to ban Jonang
tradition in the 17th century AD?

The Great Fifth Dalai Lama banned the Jonang school due to both
political and religious reasons:

1. The cause for the downfall of the Jonang school is generally seen in
the exegesis of Asanga's Mind-Only-School by Sherab Gyatsen, the first
great exponent of the order. He had formulated a philosophical position
that later was considered 'heretical', for it offered a way of
conceptualizing the process of Enlightenment that was close to the
thoughts of early mediaeval Chan Buddhism of the Chinese monk Hvashang.
The latter had taught the possibility of a sudden awakening of the
Enlightenment state through the absence of mental activity. This
position was to provide the pretext for proscribing the Jonang order.

This is much to do with the debates based on Rang tong and Sheng tong
views, and not forget to mention an unique Sheng tong views of the
Jonang school. I will not elaborate here as I am not a
scholarly-trained.

2. From the religious-dogmatic point of view the proponents of the
Indian Buddhist school, such as Kamasila and his students, had triumphed
over those of Hvashang’s Chinese Chan tradition. Yet, records of the
Jonangpa tradition claim the victory of the Hvashang tradition at the
Samye Council. Thus the Jonang teachings only became a deviation from
the ‘unvarnished truth’ when later Tibetan apologists identified
themselves with the Indian parties.

For better understanding on this subject, please refer to "Enlightenment
by a Single Means: Tibetan controversies on the 'Self-Sufficient White
Remedy (Dkar Po Chig Thub)" by David Jackson. From page 178 to 180,
there is a very detail Tibetan account on this debate.

3. There were some more reasons why the Jonangpa were taken between two
fires of the doctrinal disputes. Their notion that gifts to monasteries
as a means for the path to Enlightenment would be dispensable were
sowing seeds of discontent for these gifts were an important base to the
political power of several Buddhist orders, namely the rising Gelugpa.

4. The objective of power politics had the Jonangpa being on the
'politically wrong side' as they were, like the Karma-Kagyu, closely
associated with the Gelugpa’s main rivals for power in central Tibet,
the princes of Tsang. Any significant influence of the Jonangpa thus was
a thorn in the Gelugpa’s side.

During that period of time, the new central government, Ganden Phodrang,
was just formed in Lhasa. Any rivals for power from supporters of/and
the princes of Tsang, will definitely threaten the new government and
the unification of all the Tibetans.

5. Jetsun Taranatha who had been sent to Urga in Khalkha Mongolia by the
prince of Tsang, was staying there for two decades. When in 1634 he died
in Urga, his reputation endured for his reincarnation was discovered in
a son of the Khalkha Mongol prince Tusiyetu Khan. The boy was declared
to be the spiritual leader of Mongolia and given the title of "Holy
Venerable Lord" (Jetsundampa). Thus the Jonangpa, and together with them
the princes of Tsang, were about to secure the support of one of the
most mighty central Asian powers. The decisive political move was then
made by the Great Fifth Dalai Lama by eliminating the Jonangpa order,
yet expressing his support for the Jetsundampa incarnation and thus
integrating him into the Gelugpa system.

For those who are familiar with Mongolian Buddhist Arts, Under Gegen
Zanabazar, the First Bogdo Zabzundamba or Hutuktu Zabzundamba, is the
first Mongol reincarnation line of Jetsun Taranatha.

Now, in a recent article "A Survey of the Paths of Tibetan Buddhism",
His Holiness the Fourthteenth Dalai Lama, Tenzin Gyatso, wrote about the
doctrine views of the Jonangpas:

"Amongst the definitive sutras are also included sutras belonging to the
third turning of the wheel of doctrine, particularly the Tathagata
Essence Sutra, which is actually the fundamental source of such Middle
Way treatises as the Sublime Continuum and the Collection of Praises
written by Nagarjuna. Also included in the third turning were other
sutras such as the Sutra Unravelling the Thought of the Buddha, which
according to some Tibetan masters are also categorized as definitive.

These scholars (such as the Jonangpas) maintain an unique view of
emptiness, which is technically called 'emptiness of other', and they
speak of different kinds of emptiness qualifying different phenomena.
They maintain that conventional phenomena are empty of themselves and
ultimate phenomena are empty of conventional phenomena.

You could interpret this explanation of emptiness, that conventional
phenomena are empty of themselves, to mean that because conventional
phenomena are not their own ultimate nature, they are empty of
themselves. But these Tibetan scholars do not interpret it in such a
way, they maintain that because phenomena are empty of themselves, they
do not exist.

As we know from history that many masters belonging to this group of
scholars actually achieved high realizations of the generation and
completion stages of tantra, they must have had a profound understanding
of their particular interpretation of emptiness. But if we were to
interpret emptiness as things being empty of themselves in such a manner
that they do not exist at all, it would be like saying that nothing
exists at all.

Because they maintain that conventional phenomena do not exist, being
empty of themselves, they maintain that their ultimate nature is truly
existent phenomenon that exists in its own right, is inherent existent.
And when they speak of the emptiness of this ultimate truth they refer
to its being empty of being a conventional phenomenon."

So from this quotation, we can see that early Jonangpa masters are all
accomplished masters through the practice of tantric Vajrayana
teachings. And they do not interpret it in such a way like those
standard Rang tong and Shen tong explanations. Thus, in the official
website for Dorje Ling Buddhist Center, a Jonangpa Dharma centre, wrote
"The Jonangpa tradition is famous because of its strong historical
connection dedicated to the instruction and practice of Kalachakra
Tantra. The Jonang tradition differs from other Buddhist schools of
thought due to its philosophical viewpoint on the nature of reality".

Your Dharma pal,
Geleg-la.