feat(context): reasoning-thread continuity, L3 doc filtering, and gate hardening

Threads reasoning_content across inference calls and journal renders, filters
markdown noise out of L3 repo-knowledge retrieval, adds PlanLinter H3 checks,
and tightens filesystem tool output/dir-listing behavior surfaced by prior
live QA (see project_readloop_campaign memory).

examples/workflows/prompts/architect_freestyle.md

@@ -85,6 +85,27 @@ Emit a JSON object that validates against the `execution_plan` schema:
   Those fetch remote code and prompt on stdin; the run is unattended (no TTY) so they hang, and
   `shell` rejects them outright. `shell` in a scaffold stage is for `npm install` / `npm run
   build` on files that already exist, not for generating the project.
+- **Every stage prompt must describe its exact JSON output structure when using a
+  structured kind.** The model that runs the stage never sees the raw JSON schema — it only sees
+  the kind's name (e.g. `analysis`, `research_report`, `review_report`) and the prompt you write
+  here. Therefore each stage prompt must:
+  - Conclude with a `Call \`emit_artifact\` with a JSON object matching this shape:` line
+    followed by the literal JSON structure the kind expects (fields, types, required vs
+    optional).
+  - When the kind is `file_written` no `emit_artifact` is needed — the stage writes files
+    directly. For all other kinds, the prompt must spell out the exact JSON schema inline.
+  - Include at least one concrete example JSON object matching the schema, so the model has
+    a template to follow.
+  - For reference, the available JSON schemas and their shapes are: `discovery`
+    (`{ready: boolean, questions: [{prompt, options?, multiSelect?, header?}]}`),
+    `analysis` (`{goal, constraints: [{description, severity}], risks:
+    [{description, severity, mitigation?}], open_questions: [{question, answered?}]}`),
+    `design` (`{approach, architecture: [{component, responsibility, interfaces}],
+    plan: [{step, action, files: [path]}]}`),
+    `impl_plan` (`{overview, steps: [{action, target, details}]}`),
+    `research_report` (`{summary, findings: [string], sources: [string]}`),
+    `review_report` (`{verdict, notes}`). Use these shapes verbatim in the
+    prompt — do not paraphrase or omit fields.
 
 **edges** — describe every transition between stages. Rules:
 - `from` and `to` must each be a declared stage `id` or the literal string `"done"`.