In theory and practice, every new line of code that a company such as Transparen writes is an intellectual property asset.  This is in theory because the rights are protected, but not every bank or financial institution would regard intellectual property as a very good form of security.  It is also in practice because it is intellectual property that enables a company such as Transparen to charge clients less than the cost of development of a customized or completely custom-made product - reselling intellectual property in some form bridges the gap between what clients are willing to pay and what software actually costs to make.

All of the above is very interesting, but it does not solve the problem of financing such a software project which is only partly funded by a client.

Part of the answer is to issue more shares as the development continues, and to sell those shares - possibly to the customer, and possibly to another investor.  But someone must buy those new shares, or development cannot continue because it would not be adequately funded.

Also, if possible, additional clients should be brought on board to purchase licenses to the software - in this way, if enough clients are found, then the company may be able to purchase its own shares (or avoid issuing the shares).