A program is not a passive thing like a book. A book is created by the author, and you the user run through the book at your own speed, but every word you are going to read is pre-determined, fixed, and unchanging. Software by its nature is interactive both from a data point of view, and also by the operation of the various options and commands. The more flexible and changeable the commands are, the more you will call it "malleable". Just like people add accessories to cars, there are software products most notably Photoshop, which enables thousands of plug-ins to achieve additional function.
There is no reason why isolated apps have to stay isolated. We can (gasp) attempt to standardize on a protected arithmetic, and universal data interchange that is more robust than stupid JSON, which is a terribly weak interchange standard. Microsoft and Apple both put a lot of effort into intra-application communication, but unfortunately, Google and other web companies have spent most of their waking minutes trying to starve Apple, Adobe, and MS of their air supply by offering free versions of their core software with the goal of undermining their economic foundations. In essence, Google maintains a near monopoly on search and advertising revenue, and with their vast surpluses engages in predatory attacks on traditional companies, all under the banner of "Free! Free! Free!". Free until you want to get clicks for your company or service, then you find out how dear those clicks are.
And now we have Amazon becoming a dominant player in cloud hosting, taking its vast surplus from selling to government extremely expensive secure racks that somehow are mandated by security regulations, and predating upon the data center market. In a recent visit to my racks in Fremont at a smaller competitor, it was half empty. I calculated that Amazon is more than 10x more expensive than doing it yourself, but now Amazon is proliferating options, and configuration tools that lock you in. So when you say malleable software, what part is malleable? It practically takes 1000 hours now just to understand Amazon's catalog.
The overwhelming thrust of the current market is to increase complexity to such a ridiculous level that opening up a piece of software may not be that helpful, if you have to not only understand the code you are looking at, but also understand this tall tower of supporting tools and remote services.
My point is that a dramatic simplification is the first order of business, then you can make things very malleable, and have more flexible, personally customized products. There is indeed no good reason why things can't evolve towards more malleability, but i am asserting we are heading in the opposite direction at present inadvertently due to the complexification.