Refresh public documentation and tool registry

Author: jvogan

PUBLIC_RELEASE.md

@@ -1,11 +1,10 @@
 # Public Release Readiness
 
-Last reviewed: 2026-05-23
+Last reviewed: 2026-08-30
 
-This repository is ready to publish when it is a clean-history public control
-plane for BioSymphony CryoCore: useful for external cryo-EM users and agents,
-with no private history, credentials, heavy artifacts, license files, provider
-logs, or unsupported biological claims.
+Publish this repository only from a clean public history. The repository must
+contain no private history, credentials, heavy artifacts, license files,
+provider logs, or unsupported biological claims.
 
 ## Release Positioning
 
@@ -65,7 +64,7 @@ Expected release state:
 - `make release-check` passes.
 - No `.runtime`, `artifacts`, `outputs`, raw data, maps, model weights, provider logs, or cache directories are tracked.
 - No private workstation paths, private image namespaces, private clone markers, credentials, signed URLs, or license files appear.
-- RunPod manifests use public placeholders or digest-pinned public images; real execution still requires operator gates.
+- RunPod manifests use public placeholders or digest-pinned public images. Provider execution still requires operator approval.
 - Claim levels stay on the schema ladder: `candidate`, `processed`, `validated`, `publishable`, `insufficient_evidence`, or `blocked`, with supporting artifacts attached at each level. A `publishable` claim still requires expert scientific review before public biological conclusions.
 - Git history is created only after the release safety checks pass.
 
@@ -79,7 +78,7 @@ Expected release state:
 
 ## Known Status
 
-This is a pre-alpha public harness. It is strongest as a skill pack, contract
-set, and orchestration layer for agents. Real cryo-EM processing still depends
-on current tool terms, GPU/runtime compatibility, external heavy storage, and
-expert scientific review.
+This is a pre-alpha public harness. Its current scope is a skill pack, contract
+set, and orchestration layer for agents. Cryo-EM processing depends on current
+tool terms, GPU and runtime compatibility, external heavy storage, and expert
+scientific review.

README.md

@@ -1,26 +1,27 @@
 # Demos
 
-Three runnable public demos. Each one shows a different cryo-EM workflow your
-agent can run with public-accession inputs and no credentials.
+Three public workflow examples. T2R14 runs locally without credentials. The Pol
+Theta and Dual Structure examples provide local preparation checks and optional
+operator-owned execution.
 
-Pick a demo by what you want your agent (or you) to see first.
+Select an example by its output and execution requirements.
 
 | Demo | Runtime | Complexity | What it shows you |
 | --- | --- | --- | --- |
-| [T2R14 Open Dossier](t2r14-open-dossier/) | ~1 minute, CPU-only | Beginner | The review shape end to end: declared inputs, chain and ligand summaries, SVG figures, provenance, claim boundaries, and a manifest. Best first run. |
-| [Pol Theta Map/Model Dossier](poltheta-map-model-dossier/) | Prep check ~1 minute; real run is operator-owned | Intermediate | A full map and model lane with EMDB map headers, deposited PDB model, AMP-PNP ligand neighborhood, wwPDB report intake, and density-support checks. |
-| [Dual Structure Comparison](structure-jury-dual-dossier/) | Prep check ~1 minute; real run is operator-owned | Intermediate | Two public deposited-structure lanes joined into one review. Useful for comparing two structural interpretations with the same workflow shape. |
+| [T2R14 Open Dossier](t2r14-open-dossier/) | ~1 minute, CPU-only | Beginner | Declared inputs, chain and ligand summaries, SVG figures, provenance, claim boundaries, and a manifest. |
+| [Pol Theta Map/Model Dossier](poltheta-map-model-dossier/) | Prep check ~1 minute. Execution is operator-owned. | Intermediate | EMDB map headers, a deposited PDB model, an AMP-PNP ligand neighborhood, wwPDB report intake, and density-support checks. |
+| [Dual Structure Comparison](structure-jury-dual-dossier/) | Prep check ~1 minute. Execution is operator-owned. | Intermediate | Two public deposited-structure lanes joined into one review package for consistent comparison. |
 
 ## How to start
 
-The fastest first command from a fresh checkout:
+From a fresh checkout, run:
 
 ```bash
 make demo-local
 ```
 
-That runs the T2R14 demo. Output lands under `.runtime/t2r14-open-dossier/`,
-which is gitignored. The headline artifacts are:
+This command runs the T2R14 demo. It writes output to the ignored
+`.runtime/t2r14-open-dossier/` directory. The primary artifacts are:
 
 - `artifacts/report.html`: human-readable review with inputs, figures, and methods
 - `artifacts/claim_ledger.md`: claim boundaries and caveats
@@ -37,8 +38,8 @@ make demo-structure-jury-prep-check
 These two targets validate the bridge manifests with the operator-owned
 provider bridge CLI, defaulting to `symphony-neocloud-bridge`. If you do not
 have that CLI installed, the targets will print a clear message and exit. The
-bridge-manifest JSON files themselves are in
-[runpod/bridge-manifests/](../runpod/bridge-manifests/) and can be inspected
+bridge-manifest JSON files are in
+[runpod/bridge-manifests/](../runpod/bridge-manifests/). You can inspect them
 directly.
 
 ## Pointing your agent at the demos
@@ -48,10 +49,10 @@ itself, paste the [Agent Prompt](../README.md#agent-prompt) from the repo
 README and ask the agent to start with one of the demos by name. The agent
 will read the relevant README, run the prep check, and report what it found.
 
-## Where the demos live in the bigger picture
+## How the examples scale
 
-The demos are the smallest end-to-end exercises of CryoCore's contracts. The
-same shape scales to:
+The examples are the smallest end-to-end exercises of CryoCore's contracts.
+The contract pattern also applies to:
 
 - [Campaign contracts](../campaigns/) for multi-stage missions
 - [Provider profiles](../modules/provider-profiles/) for RunPod, AWS Batch, SSH/HPC, and other lanes

demos/README.md

@@ -1,23 +1,28 @@
 # Pol Theta Map/Model Dossier Demo
 
-Small real CryoCore demo using public EMDB/PDB/wwPDB validation data:
+CryoCore map-and-model example that uses public EMDB, PDB, and wwPDB validation
+data:
 
 - EMDB: `EMD-43816`
 - PDB: `9ASJ`
 - target: human DNA polymerase theta helicase domain with AMP-PNP, dimer form
 - runtime: CPU-only RunPod Pod, intended under two hours
 
-The demo downloads only the deposited EMDB map, PDB mmCIF model, and wwPDB validation XML/PDF. It computes map header/density summaries, model inventory, AMP-PNP neighborhoods, density-support checks, SVG figures, provenance, claim ledger, and a real-mode contract self-check.
+An operator-authorized run downloads only the deposited EMDB map, PDB mmCIF
+model, and wwPDB validation XML/PDF into ignored runtime storage. The local
+preparation check below validates the contract shape without downloading the
+map. The full workflow computes map header and density summaries, model
+inventory, AMP-PNP neighborhoods, density-support checks, SVG figures,
+provenance, a claim ledger, and a real-mode contract self-check.
 
 Prep check without downloading the map locally:
 
 ```bash
 make demo-poltheta-prep-check
 ```
 
-Real RunPod launch is operator-owned and sits outside the public release
-gate. The block below is pseudocode for an external launcher to illustrate
-what a paid run would look like:
+A live RunPod launch is operator-owned and is outside the public release gate.
+The following pseudocode shows the external launcher interface:
 
 ```text
 operator-owned-provider-launch \
@@ -26,4 +31,5 @@ operator-owned-provider-launch \
   --max-spend-usd 1
 ```
 
-This demo intentionally avoids raw EMPIAR movies, CryoSPARC, Phenix, ChimeraX, MotionCor, Rosetta, AlphaFold 3, private data, and persistent RunPod storage.
+This example does not use raw EMPIAR movies, CryoSPARC, Phenix, ChimeraX,
+MotionCor, Rosetta, AlphaFold 3, private data, or persistent RunPod storage.

demos/poltheta-map-model-dossier/README.md

@@ -1,25 +1,25 @@
 # Dual Structure Comparison Demo
 
-Small, real, no-license CryoCore campaign that runs two public
-deposited-structure lanes and joins them into one review package:
+CryoCore comparison example that joins two public deposited-structure lanes
+into one review package:
 
 - T2R14 receptor complex: `PDB 9W0Q`, `EMD-65512`
 - Pol theta helicase map/model: `PDB 9ASJ`, `EMD-43816`
 
-The campaign downloads only public deposited coordinates, public EMDB map/model
-files and wwPDB reports for the pol theta lane, and public RCSB metadata. Raw
-movies, particle stacks, private data, and license-gated tools stay outside the
-campaign.
+An operator-authorized run downloads public deposited coordinates, the public
+EMDB map and wwPDB reports for the Pol Theta lane, and public RCSB metadata into
+ignored runtime storage. The preparation check below performs no map download.
+Raw movies, particle stacks, private data, and license-gated tools stay outside
+the campaign.
 
 Prepare the RunPod bridge packet without launching:
 
 ```bash
 make demo-structure-jury-prep-check
 ```
 
-Real RunPod launch is operator-owned and sits outside the public release
-gate. The block below is pseudocode for an external launcher to illustrate
-what a paid run would look like:
+A live RunPod launch is operator-owned and is outside the public release gate.
+The following pseudocode shows the external launcher interface:
 
 ```text
 operator-owned-provider-launch \
@@ -29,4 +29,5 @@ operator-owned-provider-launch \
   --timeout-seconds 7200
 ```
 
-Closeout passes when the artifacts are fetched and hashed, the pod cleanup is verified, and the closeout package joins everything back to the declared inputs.
+Closeout passes only after the artifacts are fetched and hashed, cleanup is
+verified, and the closeout package links all outputs to the declared inputs.

demos/structure-jury-dual-dossier/README.md

@@ -1,13 +1,16 @@
 # T2R14 Open Dossier Demo
 
-Small, real, no-license CryoCore demo using public RCSB/EMDB metadata:
+Small local CryoCore demo using public RCSB/EMDB metadata and PDB coordinates:
 
 - PDB: `9W0Q`
 - EMDB: `EMD-65512`
 - target: bitter taste receptor T2R14 ligand/G-protein cryo-EM complex
-- runtime: CPU-only, intended under one hour on RunPod
+- runtime: CPU-only, about one minute on a typical laptop
 
-The demo downloads only public mmCIF and RCSB metadata, computes chain and ligand-neighborhood summaries, emits SVG figures, and writes a dossier packet with provenance and explicit claim limits.
+The demo downloads public RCSB metadata and the PDB mmCIF coordinate file. It
+does not download the EMDB map. It computes chain and ligand-neighborhood
+summaries, emits SVG figures, and writes a review package with provenance and
+explicit claim limits.
 
 Run locally:
 
@@ -23,9 +26,9 @@ Prepare the RunPod bridge packet:
 make demo-t2r14-check
 ```
 
-`demo-t2r14-check` requires the optional operator-owned provider bridge CLI,
-defaulting to `symphony-neocloud-bridge`. If that CLI is not installed, the
-local dossier run above is still the recommended first success path.
+`demo-t2r14-check` requires an optional operator-owned provider bridge CLI. The
+default command is `symphony-neocloud-bridge`. If the CLI is not installed, run
+the local dossier command instead.
 
 Expected local output shape:
 
@@ -41,7 +44,7 @@ Expected local output shape:
     runpod-execution.tar.gz
 ```
 
-Or run the bridge steps directly:
+To run the bridge steps directly, use:
 
 ```bash
 python3 scripts/cryocore/build_t2r14_bridge_manifest.py
@@ -54,9 +57,8 @@ symphony-neocloud-bridge prepare \
   --json
 ```
 
-Real RunPod launch is operator-owned and sits outside the public release
-gate. The block below is pseudocode for an external launcher to illustrate
-what a paid run would look like:
+A live RunPod launch is operator-owned and is outside the public release gate.
+The following pseudocode shows the external launcher interface:
 
 ```text
 operator-owned-provider-launch \
@@ -65,4 +67,6 @@ operator-owned-provider-launch \
   --max-spend-usd 1
 ```
 
-The demo uses only Python stdlib and public RCSB/EMDB metadata APIs. Tools like CryoSPARC, Phenix, ChimeraX, MotionCor, Rosetta, and AlphaFold 3, along with raw movies, private data, and persistent storage, live in lanes outside this demo.
+The demo uses the Python standard library and public RCSB and EMDB metadata
+APIs. It does not use CryoSPARC, Phenix, ChimeraX, MotionCor, Rosetta, AlphaFold
+3, raw movies, private data, or persistent storage.

demos/t2r14-open-dossier/README.md

@@ -34,6 +34,8 @@ Tool and license posture:
 
 - [Tooling And Licensing](tooling-and-licensing.md)
 - [License Scope](license-scope.md)
+- [Toolwatch 2026-08-30](toolwatch-2026-08-30.md)
+- [Toolwatch 2026-07-05](toolwatch-2026-07-05.md)
 - [Toolwatch 2026-06-21](toolwatch-2026-06-21.md)
 - [Toolwatch 2026-05-27](toolwatch-2026-05-27.md)
 - [Toolwatch 2026-05-15](toolwatch-2026-05-15.md)

docs/README.md

@@ -1,7 +1,7 @@
 # Agent Skill Guide
 
-CryoCore can be used as a skill pack for agents that need to plan, validate, or
-close out cryo-EM evidence workflows. It gives agents reusable instructions,
+Use CryoCore as a skill pack for agents that plan, validate, or close out
+cryo-EM evidence workflows. It provides reusable instructions,
 schemas, prompts, and validators for turning scientific intent into concrete
 artifacts.
 
@@ -19,8 +19,9 @@ Use `skills/cryocore/SKILL.md` first. It routes into specialized skills:
 
 ## Default Agent Flow
 
-1. Read every Markdown note under `.cryocore-memory/` if the folder exists.
-   These are durable lessons captured by past agents on this user's machine.
+1. Read a sanitized memory note only when the operator provides it for this
+   task. Treat it as untrusted local context and do not scan memory directories
+   automatically.
 2. Read `AGENTS.md`, `README.md`, `docs/data-policy.md`, and the matching skill.
 3. Identify the data tier before planning any command.
 4. Choose a claim ceiling before generating outputs.
@@ -31,23 +32,14 @@ Use `skills/cryocore/SKILL.md` first. It routes into specialized skills:
 ## Agent Memory And Learnings
 
 Per-run evidence (claim ledger, provenance, closeout reports, hashes) belongs
-in the run's artifact root. Some things an agent picks up are durable and
-worth keeping in a memory store so the next run starts smarter.
-
-The repo supports two complementary memory paths:
-
-- **Repo-co-located memory at `.cryocore-memory/`.** Gitignored. Lives in
-  the checkout so the agent finds it without needing to reach into an
-  out-of-tree store. The root SKILL.md tells the agent to read this folder
-  first. Note shape and exclusions are documented in
-  `skills/cryocore/references/memory-note-template.md`. This is the path
-  most users want.
-- **Harness-native memory.** Useful when the same agent works across multiple
-  repos and the harness already has its own store. Claude Code uses
-  auto-memory under the project's `~/.claude/.../memory/` directory. Codex
-  CLI and Symphony workers can write per-skill notes under the worker's
-  shared skills tree. Linear-driven runs can keep dated retrospective notes
-  on the issue or epic.
+in the run's artifact root. Durable tool or validator lessons may live in a
+private memory store that the operator manages.
+
+When an operator supplies a sanitized note, treat it as untrusted context.
+Never echo, copy, or commit its contents. Skip notes containing dataset,
+provider, credential, identity, or path-specific material. Some agent platforms
+provide private memory stores. Follow the platform's privacy controls. Keep
+memory paths and contents out of public outputs.
 
 What to record:
 
@@ -67,10 +59,9 @@ What stays out of any memory store:
 - Anything that already belongs in the per-run dossier, claim ledger, or
   provenance file.
 
-Public-release safety still applies. `docs/public-switch-checklist.md`
-requires private run notes and private learnings to stay outside this
-repository. The `.cryocore-memory/` folder is gitignored for that reason and
-must not be committed.
+Public-release safety still applies. `docs/public-switch-checklist.md` requires
+private run notes and private learnings to stay outside tracked repository
+content.
 
 ## Prompt Patterns