feat(core): add first-class Pi session indexing (#23)

Pi cannot be read as another linear JSONL stream. Its history is a tree with
a durable leaf, orphan roots, branch summaries, and two compaction forms, so
the active context is something the format states rather than something line
order implies. The adapter keeps those semantics inside itself and projects
the result into the existing canonical tables.

Sessions are keyed by (normalized header cwd, header id) rather than by path,
because Pi's --session-id lookup is project-local: two projects may reuse an
id, while a move or an identical copy is still one session. Discovery covers
both layouts Pi writes and fingerprints each file by mtime, ctime, size and
inode, so a rewrite that preserves mtime is not read as unchanged.

Abandoned branches are preserved rather than dropped. Visibility becomes
three-state -- visible, inactive, hidden -- and helpers return only visible
rows until includeInactive asks for the superseded path, labeling every row
so a caller knows which it holds. Usage counts all three, because an
abandoned call still spent tokens; message_count reports only the visible
transcript.

A committed MIT-licensed oracle transcribed from Pi 0.83.0 pins the context
algorithms, and a fixed-seed differential runs 512 generated sessions against
it on every test run. Schema changes are additive.

skill-doc/references/query-patterns.md

@@ -349,6 +349,7 @@ for (const { facet, terms } of learnedFacets) {
     JOIN sessions s ON s.id = m.session_id
     WHERE m.session_id IN (${sessionIds.map(() => '?').join(',')})
       AND m.text IS NOT NULL
+      AND COALESCE(m.visibility, 'visible') = 'visible'
       AND (${clauses})
     ORDER BY m.timestamp
     LIMIT 3
@@ -448,6 +449,7 @@ const before = sql(
   `SELECT uuid, role, timestamp, substr(text,1,200) AS snippet
    FROM messages
    WHERE session_id=? AND timestamp<?
+     AND COALESCE(visibility, 'visible') = 'visible'
    ORDER BY timestamp DESC LIMIT 3`,
   s.session_id,
   s.timestamp
@@ -456,6 +458,7 @@ const after = sql(
   `SELECT uuid, role, timestamp, substr(text,1,200) AS snippet
    FROM messages
    WHERE session_id=? AND timestamp>?
+     AND COALESCE(visibility, 'visible') = 'visible'
    ORDER BY timestamp ASC LIMIT 3`,
   s.session_id,
   s.timestamp
@@ -532,6 +535,7 @@ const counts = sql(`
   JOIN messages m ON m.uuid = tr.message_uuid
   JOIN sessions s ON s.id = tr.session_id
   WHERE tr.is_error = 1
+    AND COALESCE(m.visibility, 'visible') = 'visible'
     AND s.project LIKE ?
   GROUP BY tc.name
   ORDER BY failure_count DESC, last_failure_at DESC
@@ -551,6 +555,7 @@ const examples = sql(`
   JOIN messages m ON m.uuid = tr.message_uuid
   JOIN sessions s ON s.id = tr.session_id
   WHERE tr.is_error = 1
+    AND COALESCE(m.visibility, 'visible') = 'visible'
     AND s.project LIKE ?
   ORDER BY m.timestamp DESC
   LIMIT 8
@@ -580,6 +585,7 @@ const groups = sql(`
   JOIN messages m ON m.uuid = tr.message_uuid
   JOIN sessions s ON s.id = tr.session_id
   WHERE tr.is_error = 1
+    AND COALESCE(m.visibility, 'visible') = 'visible'
     AND s.project LIKE ?
   GROUP BY s.id
   ORDER BY last_failure_at DESC
@@ -598,6 +604,7 @@ const examples = sql(`
   JOIN messages m ON m.uuid = tr.message_uuid
   JOIN sessions s ON s.id = tr.session_id
   WHERE tr.is_error = 1
+    AND COALESCE(m.visibility, 'visible') = 'visible'
     AND s.project LIKE ?
   ORDER BY m.timestamp DESC
   LIMIT 12
@@ -694,6 +701,7 @@ const row = sql(`
   SELECT uuid, length(text) AS indexed_len
   FROM messages
   WHERE length(text) >= 10000
+    AND COALESCE(visibility, 'visible') = 'visible'
   LIMIT 1
 `)[0];
 if (!row) return null;