Reorganize packages into a modular hierarchy

Move the 18 flat packages/<name> packages into role-grouped dirs:
core/, llm/, bash/, session-persistence/, ui/, support/. Group dirs are
pure containers; each package keeps its @deepseek-ai/dsh-* name.

Collapse the per-package tsconfig paths maps (base + typecheck) into one
@deepseek-ai/dsh-* wildcard with a candidate per group, and derive the
publint list from the hierarchy. Update all depth-coupled globs/configs
(workspace, tsdown, vitest, eslint, knip, tsconfig includes/refs,
per-package tsconfigs, generators, doc-script scopes, type-equiv manifest)
and the cross-package/script relative imports in tests.

Fix doc-typecheck's workspacePaths() to parse tsconfig JSONC via the
TypeScript API instead of a regex comment-strip, which corrupted the
new wildcard `/*/` path candidates.

WIP: doc cross-links and package/RFC docs still to update.

packages/session-persistence/session-persistence-sqlite/README.md

@@ -0,0 +1,29 @@
+# @deepseek-ai/dsh-session-persistence-sqlite
+
+A SQLite durable session-persistence backend — a second `SessionPersistence` implementation ([session persistence](../../docs/rfc/implemented/2026-06-14-session-persistence.md)), built to validate that the abstract seam and the shared `runPersistenceContract` suite are genuinely backend-agnostic. It satisfies the SAME contract as `dsh-session-persistence-jsonl` (append-only, contiguous-seq, lazy materialization, interrupted-turn close on load), expressed over `node:sqlite` rows instead of file bytes.
+
+> **TODO:** this backend talks to `node:sqlite` directly. If a cordis database service (`cordis/db` / a `@cordisjs` SQL driver plugin) is adopted, route through that instead of holding a raw `DatabaseSync` here — the contract surface (`SessionPersistence`) would not change, only the storage driver.
+
+## Storage model
+
+Each `SessionEvent` maps 1:1 onto a row in an `events` table `(session_id, seq, type, time, data)` — `data` is the event payload as JSON text, so the row shape is the event verbatim (including `assistant/chunk`, keeping `seq` contiguous). Out-of-log metadata (`SessionHeader`) lives in a `sessions` row. A `sessions` row is written only by the first `append` — its existence is the lazy-materialization signal (`has`/`list` report exactly the sessions that have a row), so no separate column is needed.
+
+The repo targets Node ≥ 24 (the root `engines` field), which includes the stable `node:sqlite` module. The database opens with `foreign_keys = ON` (so `ON DELETE CASCADE` drops a session's events with its row) and `journal_mode = WAL`. The table-layout version is stored in `PRAGMA user_version` and checked on open: a fresh database is stamped with the current `SCHEMA_VERSION`; a database written by any other, incompatible build (a non-current `user_version`, older or newer) is rejected rather than opened against an unknown layout — there is no migration (unreleased software).
+
+## Contract semantics over rows
+
+- **Append = a transaction.** `append` runs `BEGIN`/`COMMIT` around the batch: it materializes the `sessions` row (if still lazy) and INSERTs every event, asserting the contiguous-seq contract first (the first event's `seq` must equal the stored next-seq). A mid-batch failure (a UNIQUE violation on a duplicated seq) rolls back entirely, so the stored log and the in-memory cursor stay consistent. (`load()` already balanced the stored log, so `append` never has to repair a crash tail.)
+- **Lazy materialization.** `create()` records intent in memory only — no row is written until the first `append`. A created-but-never-appended session has no `sessions` row, so it is absent from `has()`/`list()` (which report exactly the sessions that have a row).
+- **Interrupted-turn close on load.** `load()` reads every stored event ordered by `seq` and finds the longest seq-contiguous, parseable prefix — INCLUDING the real events of an interrupted final turn after the last `turn/end` (the loop only flushes at `turn/end`, so a process killed mid-turn leaves real, fully-written rows past it). A single turn can be huge in a long-horizon task, so those events are **preserved, never truncated**: `load()` CLOSES the orphaned turn by durably appending the minimal synthetic boundary events (an error `tool/result` for every assistant tool call left unanswered, a `step/end` if a step was open, then a `turn/end` carrying `{ kind: 'interrupted' }`), inside one transaction that also DELETEs any never-fully-written torn tail row. `load()` is therefore mutating — after it the stored rows are balanced and the cursor is truthful, so the next `append` continues cleanly. The boundary (last `turn/end`, torn-tail detection) is computed from the `seq`/`type` columns so a malformed `data` in a torn tail row is never parsed (discarded, not unloadable). A parse error or `seq` gap inside the committed region (at or before the last real `turn/end`) makes the session unloadable. A session whose only turn never closed keeps its metadata row and stays present in `has()`/`list()` — the same as the JSONL backend, whose file likewise survives a first append that never reached `turn/end`.
+
+## Configuration (schemastery)
+
+```ts
+interface Config {
+  path: string   // SQLite database file path, or ':memory:' for an in-process DB
+}
+```
+
+## Write path
+
+Like the JSONL backend, the plugin also installs the `session/event` → buffer → `session/flush` drain: it snapshots each event when buffered (the live `session.events` object is mutable), persists a fork's seed once on `session/created`, keeps a per-session write cursor so a resumed session never re-appends stored events, and seeds existing live sessions on apply (HMR does not replay `session/created`). Dispose awaits every in-flight init + final drain and then closes the database, so no write lands after teardown.