Give files their due
A small collection of project notes is easy to read, edit, copy and version. For one person using one assistant, a short set of conventions and decisions may be enough.
Files can also carry structured metadata and support sophisticated software. The limitation is not the file extension. It is the work your surrounding system does with the content.
Where the work becomes harder
Suppose a customer changes their terms. Some notes contain the old agreement, others the new one, and a private explanation belongs to one manager. Someone must establish which version applies and who may see it.
Search can find those passages. A managed belief layer can represent ownership, uncertainty and changes explicitly. It still needs good evidence and enforcement to make that useful.
Choose the simpler system that does the job
Stay with notes when the material is small, you can maintain it and access boundaries are straightforward. Consider a persistent Mind when several tools, agents, owners or evolving decisions make manual curation costly.
Compare setup effort, correction, retrieval quality, privacy and exit. Do not replace a working notebook merely because another product calls itself cognitive.
The end state is not either/or
The right architecture usually keeps both layers, which is what most "files versus a system" arguments miss. Keep the small, always-on index, the few hundred words of who-you-are and how-to-behave; a runtime should not throw that away. Put the deep store behind a single retrieval call instead of loading it all into context.
For one mind, that deep store can be a folder and a script, and that is the right call. It earns its way into a shared, queryable, identity-aware runtime precisely when it has to serve many minds with scope, not simply when it gets large.
thinqOS uses this same notebook pattern internally, as a complementary layer: agents keep a shared-file memory they read and write directly, sitting alongside the managed belief layer above, rather than one replacing the other.