Small systems rarely become confusing because of one dramatic choice. More often, they collect reasonable exceptions: a second place for configuration, an undocumented scheduled task, a service that can only be restarted from memory. Each addition works. The overall picture gradually disappears.
Legibility means being able to answer a few ordinary questions without reconstructing the system from clues. What is running? Where does its configuration live? What depends on it? How will a failure be noticed? How can the last known-good state be restored?
Keep one obvious path
For every recurring operation, choose one normal path and make it easy to discover. There can be emergency alternatives, but they should not compete with the routine method. A short command beside the relevant configuration is better than a perfect command hidden in shell history.
The same applies to state. If configuration is split across files, environment values, and an administrative screen, record which source is authoritative. The goal is not to force everything into one file. It is to prevent two sources from quietly claiming the same responsibility.
A useful test: could you explain the system accurately after six months away, using only what is stored beside it?
Make change visible
A small change log is often enough. It does not need release ceremony; a dated sentence that records the reason for a change can preserve the context that a configuration diff cannot. When the reason is no longer true, the sentence also makes the old choice easier to remove.
Prefer checks that expose the system from the outside: whether an expected response arrives, whether a backup can be read, whether a scheduled result was actually produced. A process being present is useful evidence, but it is not the same as the service doing its job.
Remove stale decisions
Documentation alone cannot make an overgrown system clear. Old paths, disabled fragments, and temporary workarounds still impose a reading cost. When an exception is no longer needed, remove both the exception and the explanation for it. A smaller current truth is more valuable than a complete history mixed into active configuration.
Legibility is not a one-time cleanup. It is a maintenance budget: a few minutes during each change to leave the system easier to inspect than it would otherwise be.