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.

scripts/gen-module-graph.ts

@@ -4,7 +4,7 @@
  * The architectural shape of the harness lives implicitly in each package's
  * `peerDependencies` — the canonical runtime-dependency signal (devDeps mirror
  * these as `workspace:^` plus test-only extras, which would add noise). This
- * script reads every `packages/* /package.json`, keeps only the
+ * script reads every `packages/* /* /package.json`, keeps only the
  * `@deepseek-ai/dsh-*` peer edges (dropping the `cordis` peer), and renders a
  * GitHub-viewable Mermaid graph plus a dependency table.
  *
@@ -34,7 +34,7 @@ interface Pkg {
 /** Read every workspace package and its `@deepseek-ai/dsh-*` peer edges. */
 function collect(): Pkg[] {
   const pkgs: Pkg[] = []
-  for (const rel of globSync('packages/*/package.json', { cwd: root })) {
+  for (const rel of globSync('packages/*/*/package.json', { cwd: root })) {
     const json = JSON.parse(readFileSync(resolve(root, rel), 'utf8')) as {
       name: string
       peerDependencies?: Record<string, string>