Log kli witness start failures and prevent startup stalls (#238) — v1.3 backport

[dhh1128]

Summary

Backport of #1477 to the 1.3 line (base v1.3.5). kli witness start could
stall during startup and did not reliably log error conditions (#238). This PR
makes the command log every startup/runtime failure visibly, eliminates the
interactive-prompt stall, and deprecates the mis-named --logfile in favor of the
accurate --logdir. Fixes #238.

The change is split into three commits so pieces can be dropped independently:

1. Close boot Keeper before Habery re-open (fix: close boot Keeper and reuse Reger to prevent LMDB double-open on Linux #1367). v1.3.5 is missing the
   ks.close() fix that the 1.2 and 2.0 lines already carry, so on Linux LMDB
   raises environment is already open in this process and the witness cannot
   start once runWitness reaches the Habery/setupHby re-open. This commit
   restores it. Note: on 1.3.5 this is a functional prerequisite, not merely
   optional — the Ensure kli witness start logs errors correctly #238 logging fix can't be exercised without it, so dropping
   this commit would also require adjusting one test.
2. Log failures + prevent non-TTY stalls (Ensure kli witness start logs errors correctly #238). Startup/runtime failures are
   logged at CRITICAL with a traceback (so they surface at the default
   --loglevel), the Habery is closed in a finally so a failed start leaves
   no stale LMDB lock, and an encrypted keystore started with no passcode on a
   non-TTY fails fast with a logged AuthError instead of blocking on an
   interactive getpass. --loglevel is normalized with .upper() so a
   lowercase level (e.g. debug) is honored.
3. Deprecate --logfile in favor of --logdir (Ensure kli witness start logs errors correctly #238). The logging backend
   derives the file name from --name and the subdirectory from its own prefix,
   so only the directory is meaningful; the old code mis-assigned the whole file
   path as the log head directory. --logfile is retained as a deprecated alias
   whose directory portion is used, with a stderr deprecation notice. Droppable
   if you'd rather not change the CLI surface in a patch release.

Tests

Regression + unit tests added to tests/app/cli/test_kli_commands.py, covering
the boot-Keeper close ordering, CRITICAL failure logging + Habery cleanup, the
non-TTY fast-fail (both the no-passcode and wrong-passcode paths), --loglevel
normalization, and --logdir/--logfile directory handling + the deprecation
notice. Each assertion was mutation-checked — reverting the corresponding fix
turns the targeted test red. The 1.3 CI does not run pytest under -n auto, so
the shared-store xdist isolation fix from #1477 is not needed here.

Relationship to #1477

Same fix as the approved #1477 (base main, 2.0), adapted to the 1.3 CLI layout
(keri.app.cli.*, absolute imports, help.ogler). Opened per your request on
#1477.

---

This code was developed with Claude (using the Opus 4.8 model, mostly). However,
I (Daniel the human) have read, reviewed, and worked the code, and I stand behind
it and take responsibility for it.

[kentbull]

I reviewed the main PR and this PR. They are both ready to go.

[dhh1128]

@kentbull — approved on 2026-07-11 and still open. Could this land on v1.3.5?

Worth flagging an inversion this has created: the 1.2 backport (#1487) merged on 2026-07-14, so the 1.2 line now carries the #238 fix while 1.3.5 and main (#1477) do not. Anyone moving 1.2 → 1.3 currently loses witness startup logging.

Unchanged from your review: three individually-droppable commits, the first being the boot-Keeper ks.close() restore (#1367) that 1.3.5 is missing — on this line that is a functional prerequisite, not optional, since the witness cannot reach a successful Habery re-open without it.