Release 2026-10-29: Arena Studio v0.101

.agents/skills/protocol-yaml/SKILL.md

@@ -55,7 +55,8 @@ it does NOT advance the protocol clock. Only `wait` commands do. Therefore:
   Editing only ONE of the pair is **masked** by the other — "the timeline won't update"
   is almost always a half-edited pair, not a render bug.
 - **Bind both fields to one anchor** (`duration: *show_dur` on both) so they can never
-  drift — the `open_dur`/`cl_dur` pattern from `protocols/fictrac_direction_test`.
+  drift — the `open_dur`/`cl_dur` pattern from `fictrac_direction_test` (private
+  `reiserlab/arena-experiments`, `protocols/shared/`).
 - Waits between two `trialParams` in one condition define how long the FIRST one
   actually shows (the second overrides it). Waits longer than the duration = intentional
   hold/blank; fine, but mean it.
@@ -163,7 +164,7 @@ rejection). Authored as an added rotational **velocity**:
   A negative frequency is a harmless no-op (warned): negate `bias_amplitude` instead.
 - `stopClosedLoop` clears the bias automatically. Reference:
   `docs/development/closed-loop-bias.md`; worked example:
-  `protocols/fictrac_bias_test.yaml`.
+  `protocols/shared/fictrac_bias_test.yaml` in the private `reiserlab/arena-experiments`.
 
 **Per-trial start position = the trialParams `frame_index` (Studio v0.91 / bridge 3.4).** A
 closed-loop trial opens on the Mode-3 `trialParams` `frame_index` (0-based, wraps mod the pattern's

arena_studio.html

@@ -3426,7 +3426,7 @@ <h2 id="modalTitle">Import error</h2>
 </div>
 
 <footer id="footer">
-  <span class="foot-left">Arena Studio v0.100 | 2026-10-28 18:40 ET · <a href="https://github.com/reiserlab/webDisplayTools" target="_blank" rel="noopener" title="webDisplayTools on GitHub: source, issues, and release notes (docs/development/arena-studio-release-notes.md)">GitHub</a></span>
+  <span class="foot-left">Arena Studio v0.101 | 2026-10-29 16:45 ET · <a href="https://github.com/reiserlab/webDisplayTools" target="_blank" rel="noopener" title="webDisplayTools on GitHub: source, issues, and release notes (docs/development/arena-studio-release-notes.md)">GitHub</a></span>
   <!-- Course-repo quick-links: open protocols / logs / patterns in a new tab.
        Hrefs built from the configured repo + bench id (updateGhQuickLinks). -->
   <span id="ghQuickLinks" title="Open the course repo on GitHub (new tab)">
@@ -10764,7 +10764,10 @@ <h2 id="modalTitle">Import error</h2>
             const key = [st.records, st.dropped, st.gaps, st.errors, st.notStored].join('/');
             if (key === Studio.telemetry.lastReport) return;
             Studio.telemetry.lastReport = key;
-            Studio.rawLog('telemetry ring: ' + st.records + ' records · ' + st.blocks + ' blocks · ' + (st.bytes / 1024).toFixed(1) + ' KiB · dropped ' + st.dropped + ' · gaps ' + st.gaps + ' · errors ' + st.errors + (st.notStored ? ' · refused by bridge ' + st.notStored : '') + (st.heapCollision ? ' · RING DISABLED (heap collision)' : '') + (st.survivedReboot ? ' · ring survived a reboot (boot #' + st.bootCount + ')' : ''), 'dim');
+            // `dropped` in the block header is the controller's LIFETIME eviction count (since
+            // its boot, mostly from before this page connected); only the growth since our
+            // first block is in-session loss. Say both, lead with the one that matters.
+            Studio.rawLog('telemetry ring: ' + st.records + ' records · ' + st.blocks + ' blocks · ' + (st.bytes / 1024).toFixed(1) + ' KiB · evicted this session ' + st.droppedSession + ' (controller lifetime ' + st.dropped + ') · gaps ' + st.gaps + ' · errors ' + st.errors + (st.notStored ? ' · refused by bridge ' + st.notStored : '') + (st.heapCollision ? ' · RING DISABLED (heap collision)' : '') + (st.survivedReboot ? ' · ring survived a reboot (boot #' + st.bootCount + ')' : ''), 'dim');
         }, 60000);
     } else {
         Studio.telemetry.drainer.rearm(); // NO_ACK first: learn the ring incarnation before freeing anything
@@ -10826,7 +10829,7 @@ <h2 id="modalTitle">Import error</h2>
         r.kind === 'cmd' ? 'CMD 0x' + r.cmd.toString(16) + ' st' + r.status + ' @' + r.tUs :
         r.kind === 'frame' ? 'FRAME idx' + r.idx + ' sd' + r.sdLoadUs + 'us spi' + r.spiUs + 'us' + (r.reqAgeUs != null ? ' age' + r.reqAgeUs + 'us sup' + r.superseded + (r.contiguous ? ' contig' : '') : '') + ' @' + r.tUs :
         r.kind === 'state' ? 'STATE ' + r.stateName + ' ' + (r.codeName || r.code) + ' ' + r.arg + ' @' + r.tUs : '?');
-    const summary = { tag: tag || 'drain', records: recs.length, blocks: blocks.length, survivedReboot: d.stats.survivedReboot, bootCount: d.stats.bootCount, dropped: d.stats.dropped, gaps: d.stats.gaps, heapCollision: !!d.stats.heapCollision, tail };
+    const summary = { tag: tag || 'drain', records: recs.length, blocks: blocks.length, survivedReboot: d.stats.survivedReboot, bootCount: d.stats.bootCount, dropped: d.stats.dropped, droppedSession: d.stats.droppedSession, gaps: d.stats.gaps, heapCollision: !!d.stats.heapCollision, tail };
     Studio.rawLog('telemetry dump (' + summary.tag + '): ' + recs.length + ' records' + (d.stats.survivedReboot ? ' — ring survived the reboot' : '') + (tail.length ? '\n  ' + tail.join('\n  ') : ''), recs.length ? 'warn' : 'dim');
     const b = Studio.session.bridge;
     if (b && b.logging) b.log({ event: 'telemetry_dump', summary, raw_blocks: rawBlocks });

course/cshl-2026/docs/fictrac.md

@@ -119,7 +119,7 @@ Closed-loop and the live scope need the **bridge** running on the rig computer:
   bridge"* to a live trace once data flows. Closed-loop trials show a green
   **CLOSED LOOP** tag.
 
-**Quick check:** load [`fictrac_direction_test`](protocols/README.md) — it runs
+**Quick check:** load [`fictrac_direction_test`](protocols/README.md) (since 2026-10-29 in the lab's private `reiserlab/arena-experiments`, `protocols/shared/`) — it runs
 open-loop motion first, then a closed-loop block that the fly steers. If the
 closed-loop block responds to nudging the ball, the bridge is working.
 

course/cshl-2026/docs/protocols/README.md

@@ -53,7 +53,8 @@ Animated pattern previews are embedded on all four protocol pages.
   FicTrac): full-field brightness, panel map, a moving bar, and LED levels
   2/5/10/20/40%. Use it to confirm a rig works after setup.
 - **`fictrac_direction_test`** — open-loop motion then a closed-loop block, to
-  confirm the [FicTrac](../fictrac.md) bridge is working.
+  confirm the [FicTrac](../fictrac.md) bridge is working. Since 2026-10-29 it lives in
+  the lab's private `reiserlab/arena-experiments` (`protocols/shared/`), not in the site library.
 - **`optomotor_led_test`** — a slow grating with the LED switched on for the
   last few seconds; the reference example of "fire a command partway through a
   trial."

docs/development/arena-studio-release-notes.md

@@ -4,6 +4,15 @@ The Studio's footer used to carry the full changelog inline; it now shows one li
 history lives here. Newest first. (Per-session engineering detail stays in
 `arena-studio-handover.md` and the design docs — this file is the user-facing what-changed list.)
 
+## v0.101 (2026-10-29) · Experiments move to the private repo; pixi run qc on rig PCs; rig-nodes 0.4.0; Studio overwrite-guard fix
+
+<!-- #288 -->
+- Rig-specific protocols and the per-rig records moved to the lab's private repos (`reiserlab/arena-experiments`, `reiserlab/scanimage-2026-bergamo`); `protocols/MOVED.md` says where each one went. The site library keeps the validation and demo protocols.
+
+<!-- #289 -->
+- **Saving over an existing repo protocol always asks first.** A browser-cache collision could skip the "Overwrite?" prompt after opening or promoting a protocol; it no longer can.
+- **The telemetry stats line now separates in-session evictions from the controller's lifetime counter**, so a large number after connecting to a long-running controller no longer looks like data loss.
+
 ## v0.100 (2026-10-28) · rig/ installs rig-nodes 0.3.0 with the host monitor; okey-cokey rig; imaging code moves to the private 2P repo
 
 <!-- #281 -->

docs/development/rig-software-repos-and-runners.md

@@ -111,7 +111,7 @@ stay as history.
 | **pyDisplayTools** | `tools/patfile.py` (pattern-file reader; the repo already has `pyPatternTools`), `nodes/arena_display.py` (Python port of `js/panel-color.js`, okey-cokey branch), the pure functions of `fictrac-bridge/bridge.py` (`Pipeline` mapping, `frame_schema_line`, `compact_arena_command`), `fictrac-bridge/fictrac_sim.py` moves to rig-nodes as a device simulator |
 | **stays** (gateway, export, composition) | `nodes/bridge_node.py`, `nodes/mcap_convert.py`, `nodes/_rows.py` (behavior_v2 `kf` rows), `nodes/export_log.py`, `nodes/rig.py` (arena composition; its generic preflight/supervision helpers are extracted to rig-nodes first), `pixi.toml`, `pixi.lock`, `.gitignore`, `tests/studio_emulator.py`, `tests/check_runlog_readers.js`, the gateway half of `tests/test_ros2_poc.py` (node-level tests move with their nodes) |
 | **stays** (arena visualization) | `nodes/viz_node.py`, `tests/test_viz_node.py`, the arena derivation in `nodes/foxglove_json.py`, `foxglove/arena-fictrac.json`, `foxglove/arena-bias.json`, `docs/foxglove-arena-layout.json`, `tools/tiff_run_to_mcap.py`; from okey-cokey: `nodes/stimulus_node.py`, `nodes/stimulus_core.py`, `nodes/dashboard_replay.py`, `tests/test_stimulus.py`, `tests/test_stimulus_live.py`, `foxglove/arena-okey-cokey.json`, `tests/fixtures/protocols-2026-10-14/*` |
-| **stays** (rig-specific config and records) | `README.md`, `WINDOWS-TEST.md`, `SCANIMAGE-DAY.md`, `scanimage-day-2026-10-16.md`, `windows-results-ww18-2026-10-15.md`, `docs/plan-b-explainer*.html`, `docs/build-standalone-explainer.py`, `docs/img/*`; from okey-cokey: `config/bias/okey-cokey-bfs-u3-51s5m.json`, `tools/okey-cokey-start.ps1`, `tools/bias-ufmf.ps1`, the `okey-cokey-*.md` run sheets, `HANDOVER-okey-cokey-2026-10-21.md`, `docs/okey-cokey-foxglove-dashboard-plan.md` |
+| **stays** (tool code and generic records) | `README.md`, `WINDOWS-TEST.md`, `docs/plan-b-explainer*.html`, `docs/build-standalone-explainer.py`, `docs/img/*`, `foxglove/arena-okey-cokey.json` (a layout `rig.py --foxglove` loads), `tools/ufmf.py`, `tools/patfile.py`. **Moved 2026-10-29 (LAB-227) to the private `reiserlab/arena-experiments` `rigs/<rig-id>/`:** `windows-results-ww18-2026-10-15.md` → `rigs/ww18/`; from okey-cokey → `rigs/ww14/`: `config/bias/okey-cokey-bfs-u3-51s5m.json`, `tools/okey-cokey-start.ps1`, `tools/bias-ufmf.ps1`, the `okey-cokey-*.md` run sheets, `HANDOVER-okey-cokey-2026-10-21.md`, `docs/okey-cokey-foxglove-dashboard-plan.md`. `SCANIMAGE-DAY.md` and `scanimage-day-2026-10-16.md` went to the private 2P repo with #284. |
 
 #### Amendment 2026-10-28: the imaging work is private
 

docs/development/telemetry-logging-reference.md

@@ -193,10 +193,10 @@ Studio v0.79 (`arena_studio.html`) or the named module; the bridge only adds the
 | `arena_command` | `js/arena-session.js:391` | > 8-byte requests (TRIAL_PARAMS) | v1 object, see §2.2 |
 | `trial_quality` | `arena_studio.html:8264` ← `js/trial-quality.js:246` `summary()` | **once, at run end, before export** (v0.78) | `threshold_us`, `target_us`, `trials[]`, `counts {pass, fail, unknown, open}`, `worst_gap_us`, `flagged_trials[]`, `unknown_trials[]`, `duplicates_dropped`, `records`. Per trial: `trial`, `pattern`, `status` (`pass`\|`fail`\|`unknown`), `duration_s`, `cmds70`, `index_changes`, `reads`, `frames`, `slow_reads`, `stalls`, `max_read_ms`, `age_gaps`, `max_age_ms`, `over_target`, `superseded`, `coverage[]` |
 | `display_gap` | `js/trial-quality.js:101` `gapEvent` → `arena_studio.html:8479` | one per gap > threshold, as it happens | `trial`, `pattern`, `seq`, `t_us`, `ms`, `kind` ∈ `sd_slow` (+ `phase`, `read_error`) · `frame_read` (+ `idx`; a slow read seen only in the FRAME record) · `frame_age` (+ `idx`; `req_age_us` > threshold). Absent from a clean run |
-| `soak` | `arena_studio.html:8317` `logSoak` | soak driver phases | `phase` ∈ `start` · `iteration-start` · `iteration-end` · `paused` · `end`; `iteration-end` carries `iteration`, `outcome`, `fault`, `stop_acked`, `postmortem`, `applied_0x70`, `duration_s`, `telemetry` (drainer stats: `ackSeq`, `lastSeq`, `records`, `blocks`, `bytes`, `gaps`, `dropped`, `errors`, `notStored`, …). **`dropped` is the controller's lifetime evicted-record counter from the block header** (1157 with `gaps: 0` in the sample = eviction before the drainer started, not in-run loss) |
+| `soak` | `arena_studio.html:8317` `logSoak` | soak driver phases | `phase` ∈ `start` · `iteration-start` · `iteration-end` · `paused` · `end`; `iteration-end` carries `iteration`, `outcome`, `fault`, `stop_acked`, `postmortem`, `applied_0x70`, `duration_s`, `telemetry` (drainer stats: `ackSeq`, `lastSeq`, `records`, `blocks`, `bytes`, `gaps`, `dropped`, `droppedSession`, `errors`, `notStored`, …). **`dropped` is the controller's lifetime evicted-record counter from the block header** (1157 with `gaps: 0` in the sample = eviction before the drainer started, not in-run loss); `droppedSession` (2026-10-29) is its growth since the drainer's first block of the ring incarnation, the in-session loss, and what the Studio's once-a-minute stats line leads with ("evicted this session N (controller lifetime M)") |
 | `sd_diag` | `arena_studio.html:8543` | `Studio.setSdDiag()` and the v0.79 connect banner | `flags`, `in_force` (GET_SD_INFO byte 29), `label` |
 | `probe` | `js/studio-postmortem.js:112` | post-mortem after a controller fault | `name`, `phase`, `cmd`, `req`, `sd`, then `dt`, `resp`, `status`, `ok`, `decoded` — or `error`, or `skipped: "capability X absent"`. The health read appears here as `name:"health"` with `decoded` |
-| `telemetry_dump` | `arena_studio.html:8580` | post-mortem | `summary {tag, records, blocks, survivedReboot, bootCount, dropped, gaps, heapCollision, tail[]}`, `raw_blocks[]` (hex) |
+| `telemetry_dump` | `arena_studio.html:8580` | post-mortem | `summary {tag, records, blocks, survivedReboot, bootCount, dropped, droppedSession, gaps, heapCollision, tail[]}`, `raw_blocks[]` (hex) |
 | `crash_report` | `arena_studio.html:8554` | post-mortem, fw flag bit 3 | `present`, `fault`, `ret_addr`, `cfsr`, `hfsr`, `bfar`, `mmfar`, `raw_hex` (junk after a HalfKay reflash — known) |
 | `health` | `arena_studio.html:5587` | **Console `chealth` only** | `source:"console"`, `health` (decoded 0xCA) |
 | `analog_loopback_sweep` | `arena_studio.html:5303` | Console Analog In panel | `channel`, `rows`, `fit`, `verdict` |

js/arena-telemetry.js

@@ -294,7 +294,9 @@
             blocks: 0,
             bytes: 0,
             gaps: 0, // seq discontinuities seen (should equal controller-reported drops)
-            dropped: 0, // controller's cumulative drop counter (last value)
+            dropped: 0, // controller's LIFETIME eviction counter (header value, since its boot)
+            droppedBase: null, // that counter at our first block of this ring incarnation
+            droppedSession: 0, // evictions since then = loss this drainer could have prevented
             errors: 0,
             notStored: 0, // rows the sink refused (ack withheld, will be re-read)
             duplicates: 0, // records re-delivered after a rearm (already stored, dropped)
@@ -339,14 +341,18 @@
                         break;
                     }
                     const rx = now();
+                    let freshRing = false;
                     // Ring incarnation check (review finding: an old ack after a power
                     // cycle would free unseen records). A different boot_count with the
                     // ring NOT marked survived ⇒ fresh ring: forget the cursor. Same
                     // incarnation after a rearm ⇒ drop records we already stored.
                     if (peekNext) {
                         peekNext = false;
                         if (st.bootCount != null && block.bootCount !== st.bootCount) {
-                            if (!block.survivedReboot) st.lastSeq = null;
+                            if (!block.survivedReboot) {
+                                st.lastSeq = null;
+                                freshRing = true;
+                            }
                             st.incarnations++;
                         }
                         if (st.lastSeq != null) {
@@ -361,6 +367,15 @@
                     st.bytes += block.bytes;
                     st.lastTNowUs = block.tNowUs;
                     st.dropped = block.dropped;
+                    // The header counter is the controller's lifetime eviction count: it
+                    // includes everything the ring evicted before this drainer ever asked
+                    // (a Studio connected hours after boot sees thousands with gaps 0).
+                    // Only the growth since our first block of this incarnation is loss
+                    // the host could have prevented, so that is what the UI reports.
+                    if (st.droppedBase == null || freshRing || block.dropped < st.droppedBase) {
+                        st.droppedBase = block.dropped;
+                    }
+                    st.droppedSession = (block.dropped - st.droppedBase) >>> 0;
                     st.bootCount = block.bootCount;
                     st.survivedReboot = block.survivedReboot;
                     st.heapCollision = block.disabledHeapCollision;
@@ -417,6 +432,8 @@
         function reset() {
             st.ackSeq = NO_ACK;
             st.lastSeq = null;
+            st.droppedBase = null;
+            st.droppedSession = 0;
             peekNext = false;
         }
 

js/studio-github.js

@@ -361,10 +361,22 @@
     // Thin executor: run one descriptor with an injected fetch. Returns
     // {ok, status, data}. Never logs the token. Kept tiny so the builders stay
     // the tested surface.
+    //
+    // `cache: 'no-store'` (2026-10-29, found on ww18 under LAB-227): the JSON and
+    // the raw form of ONE contents URL differ only in the Accept header and
+    // GitHub gives both the same ETag. After a raw read (runBytes: ?p= open,
+    // promote, previews) Chrome revalidated the stored raw entry for the later
+    // JSON request, got a 304 and handed back the raw YAML; res.json() then
+    // threw, `data` was null and every "does this file exist?" check
+    // (resolveRepoSaveTarget, the silent-fork guard) answered "no" — a changed
+    // protocol silently overwrote the repo copy with no "Overwrite?" prompt.
+    // Bypassing the HTTP cache for the JSON executor closes it in both orders:
+    // nothing JSON is ever stored, so runBytes can keep caching the bytes.
     async function run(fetchImpl, req) {
         const res = await fetchImpl(req.url, {
             method: req.method,
             headers: req.headers,
+            cache: 'no-store',
             body: req.body != null ? JSON.stringify(req.body) : undefined
         });
         let data = null;