Where Annona writes

Every file Annona creates, what is in it, and whether it can hold the text of your steps. If something is on disk and not in this table, it is a bug.

$ANNONA_HOME defaults to ~/.annona, $AKAION_HOME to ~/.akaion (the older name, kept so existing installations keep working), and the vault to ~/akaion-brain ($AKAION_BRAIN_DIR, or --brain-dir).

What the perimeter wrote

Path	Holds	Step text?
$ANNONA_HOME/policy.yaml	the policy	no
$ANNONA_HOME/ledger.jsonl	every decision: class, substrate, rule, outcome, and a digest of what crossed	no — a digest, never the text
$ANNONA_HOME/logs/annona.log	what the daemon did, rotated daily, kept 7 days	no — steps, prompts, tool arguments and shell commands appear as their size (<54 chars>). ANNONA_LOG_STEP_TEXT=1 puts them back: for debugging on fictional data
$ANNONA_HOME/link.json, $ANNONA_HOME/link/inbox/	the link to Agents Studio, and answers withheld from it	the inbox: yes, that is what it is for
$ANNONA_HOME/pairing.json	the token that pairs the window, mode 0600	no
$ANNONA_HOME/skills/	installed skills	no
$ANNONA_HOME/memory/index.sqlite	the search index over the vault	yes, as the vault does
$ANNONA_HOME/derived/	extraction artefacts for sources on a read-only mount	yes — text extracted from your documents

What the daemon and the CLI wrote

Path	Holds	Step text?
$AKAION_HOME/config.yaml	daemon settings	no
$AKAION_HOME/.key	the key that encrypts auth.json, mode 0600, created the first time credentials are saved	no
$AKAION_HOME/auth.json	cloud credentials, encrypted	no

Beside your material

Path	Holds	Step text?
.annona-cache/ next to a document	the text extracted from it, so it is read once	yes — the document's text, in the document's own folder, so the folder's class still applies
~/Documents/Annona/Inbox/ (attachments.inbox)	files attached in the window	yes, they are the files

Memory

Path	Holds	Step text?
~/akaion-brain/notes/*.md	the vault, as plain markdown	yes when runner.capture_to_brain is on (the default): every executed step becomes a local_only note — the request, the outcome and the answer
~/akaion-brain/.akaion/index.db	the vault's index, rebuilt from the notes	titles and tags

capture_to_brain: false turns that off. A local_only note leaves the machine only when you push it by hand.

Nothing is deleted for you

Uninstalling removes the program, not this. The ledger in particular is the record of what was decided and refused. See Uninstall.