@iowarp/clio-coder 0.4.8 → 0.4.9

package/CHANGELOG.md

@@ -2,6 +2,88 @@
 
 All notable changes to Clio Coder are documented in this file. The format follows [Keep a Changelog](https://keepachangelog.com/en/1.1.0/) and versions follow Semantic Versioning; pre-1.0 minor releases may include incompatible changes.
 
+## 0.4.9 - 2026-09-17
+
+### read
+
+- Read text of any size through bounded windows; count exact lines only through 32 MiB, keep a separate 20 MB (20000000 bytes) image ceiling, refuse binary/invalid UTF-8 with offsets, report file identity and observed changes, and provide honest tail continuation and numbering limits.
+
+### write and edit
+
+- Publish atomically to real symlink targets with mode preservation, before/after file identities, and explicit durability warnings. Bound previous-content diff reads and skip diffs above 1 MiB.
+- Edit refuses binary, invalid UTF-8, mixed or bare-CR endings; preserves BOM and uniform line endings; requires exact matching above 1 MiB. External writers remain unlocked.
+
+### bash
+
+- Keep the combined 16 MiB stop-on-output contract while distinguishing observed and retained bytes and reporting actual inline, offloaded, discarded, or failed retention under every output policy. Point large-output processing to run_script.
+
+### grep, find, and ls
+
+- Preserve partial search results on timeout, cancellation, and recoverable errors, with completeness, skipped counts, bounded samples, and unknown-coverage notices. Disclose fallback ignore differences and native find's uncounted symlink-directory skips while preserving fd glob behavior.
+- List symlink targets, broken links, and inspection failures explicitly. Select the alphabetical prefix asynchronously with bounded retained entries and report selection metadata.
+
+### run_script
+
+- Add direct script execution with an explicit interpreter, argv, cwd, timeout, declared environment and file references, disk-streamed stdout/stderr, bounded progress, and a run manifest under `.clio-coder/runs/`.
+- Preserve actual leader exit beside effective failure for incomplete group cleanup or pipe draining; bound post-exit draining to one second and state escaped-process limits. Keep 100 completed run records with bounded retention metadata reads and explicit skipped entries.
+
+### verify
+
+- Add explicit all/any tolerance combination and fail/match non-finite policy, safe-integer ULP bounds, lossless non-finite report spellings, reference/payload provenance, and separate execution/validation/scientific-validity judgements.
+- Add version-2 performance baseline environments and informational mismatch reports. Refuse judgement of capped output; align direct and host verification at the 32 MiB judged capture/reference ceiling.
+
+### gateway and MCP
+
+- Add find/describe/call routing for secondary builtins, extension commands, and trusted local stdio MCP, preserving inner authority, worker attestation, terminal results, and exported evidence identity.
+- Add strict user/project mcp.yaml configuration, digest-bound project trust, `clio-coder mcp list|trust|untrust`, and interactive `/mcp`. Cancel shared discovery with owned cleanup and await teardown on shutdown; exit cleanup stays client-owned.
+- Reject malformed MCP call result envelopes instead of reporting successful empty results.
+- Render structured-only MCP results in bounded model-visible text, preserving numeric source literals in both the projection and retained evidence.
+- Resolve overlapping MCP server prefixes deterministically and report conflicting tool names as unregistrable, preserving server identity and authority during lazy discovery.
+
+### model compatibility
+
+- Record the measured mini/qwopus3.8-27b-dense route's low/medium/xhigh effort vocabulary. Map high/max to xhigh and forward the explicit effort through LiteLLM to avoid the observed upstream rejection, consistent with an incompatible deployment default.
+
+### context, web, and artifacts
+
+- Keep workspace, skills, and recall on context; move documentation and recipe browsing to gateway capabilities clio_docs and clio_library.
+- Separate gateway GET-only web_read from full web_fetch requests. Move git, evidence, and credential_present behind the same gateway.
+- Move artifact behind the gateway with atomic publication and its existing terminal turn contract intact.
+
+### data
+
+- Add gateway inspection, selection, and validation for CSV/TSV and JSON/JSONL with streaming readers, explicit exact/sampled/cut views, precision and sentinel reporting, bounded captures, and actionable unsupported-format refusals.
+
+### terminal workbench
+
+- Use case-insensitive literal search terms across View resource identity and provenance, show match counts, and place the cursor at the end of an initial query. Ctrl+U clears the whole filter independently of customized cursor bindings, with one-step undo restoring the query and cursor. Workspace outputs lead with their basename and relative path; preview offers scrollable provenance with `i` and retains selection across refresh.
+- Separate Library discovery notices into a searchable `n` view that preserves the resource browser on return. Use package, entry, and member units consistently in status and footer counts; label plugin providers in recipe categories, explain package action scope, and open narrow layouts with detail visible. Notice-return guidance respects search focus, and trusted state colors survive sanitization of external metadata.
+- Preserve raw target/model fields until composer rendering, retaining recognizable target, model family, and variant suffixes at narrow widths. Sanitize identity and workspace text before abbreviation. Keep workspace identity and live worker counts visible in the footer. Fleet Runs shows current operations and compact task previews, with the full route and task, available policy and budget details, and a bounded answer excerpt available through Enter detail; complete available evidence remains inspectable through `/view`; control hints reflect the selected run's capabilities. Ordinary unvalidated completions retain an explicit unverified/validation summary, with full provenance on Enter and exceptional trust facts still visible.
+- Distinguish current worker operations from completed calls in Detailed previews while retaining pending checkpoint questions and canonical evidence.
+
+### maintenance reliability
+
+- Keep stale or unavailable addressed worker steering out of the main conversation and preserve the rejected draft. Preserve session-picker selection through filtering and undo, honor the selected row with customized confirmation, and prioritize task identity in narrow terminals.
+- Bound provider-error previews by terminal rows, retain actionable status and route advice, and distinguish provider retries from fleet retries. Keep complete available redacted diagnostics in inspection and export. On OpenAI-compatible routes, restore the error body the SDK truncates at 4000 characters when the captured response provably matches it, bounded at 65536 characters; other adapters keep the upstream cap. Replaying intermediate tool-use messages no longer attaches a successful completion footer to an earlier failed or cancelled turn.
+- Complete partial UTF-8 session writes before acknowledging entries, roll back failed appends, and retain pending durability flushes through descriptor cleanup. Validate session format and replay entries before switching owners, and prepare migrated ledgers before publishing reopened lifecycle state.
+- Keep provider deadlines and caller cancellation active through response bodies and release unread probe responses. Apply the same lifetime to native capability and embedding requests; permit native embedding fallback only for completed endpoint-unavailable responses, preserving the existing healthy vector and reranking contracts.
+- Render recognized completed worker contracts consistently in Fleet Runs and the transcript using verified receipt identity and conformance. Preserve raw evidence, partial-output disclosure and the distinction between execution, contract conformance and validation.
+- Align installed-skill activation guidance with the existing autonomy policy while preserving operator-gated marketplace installation, recipe restrictions and first-turn discovery. The corrected instructions replace contradictory wording without growing the prompt.
+- Retain scheduler ownership of workers across partial parallel startup and cancellation until their terminal cleanup settles. Keep concrete fleet-member steering, permission responses and cancellation within the addressed member or assignment retry chain instead of selecting a sibling with shared ancestry.
+- Reopen and restamp a migrated version-3 session in one atomic metadata publication, so a refused resume leaves the prior metadata intact instead of marking the candidate open under its old version.
+- Stop the boot-time tool-support warning for targets that were never probed; a cold gateway route reports nothing about its model until a probe, catalog entry or target flag states it.
+- Record fleet preflight results again, through `clio-coder doctor --fix`. Since 0.4.1 no command wrote the preflight store, so dispatch admission refused every SSH node while advising a plain `doctor` run that could not help. Plain `doctor` stays observation-only and says whether the node is recorded. Verified with a real worker dispatched to a homelab node over SSH.
+- Name write-root confinement in the dispatch refusal when it, not the runtime, removed a required tool, with the remedy for read-only or worktree runs.
+- Verify a preserved skill load when its `context` call shared a parallel tool batch. The ledger chains entries linearly, so the strict parent check failed for batched loads, the fail-closed clamp then protected everything after the activation, and the session could never compact. Found in a live WTF-P session that stalled at 80% context with `/context compact` reporting nothing to compact.
+- Record a loaded skill that declares no tool narrowing as a known selection. It was persisted as unknown, which also forced the compaction clamp for the rest of the session.
+- Title a session from the typed input when a prompt template or command expanded it. The session picker and replayed transcripts showed the expansion, so every WTF-P session read "<!-- Generated by WTF-P adapter compiler". The expansion stays the request that compaction reasserts.
+- Render one terminal row per tool line. A multi-line bash command stayed one row with a raw newline inside, and tool output kept cursor movement, backspaces and carriage returns, so the diff renderer painted every row below one row low and left bash residue over the composer border. Command previews collapse to one sanitized line and result text is neutralized before it is wrapped.
+- Bound one MCP result to 16 KiB of model context, the cap the built-in observation tools use. Only the 64 KiB session cap applied before, so a 62 KB search result entered context verbatim and two of them stalled a 131k local model. The full text is offloaded and the result names how to narrow the call or read the file in windows.
+- Name an ignored project settings layer under the Settings header of `clio-coder config inspect`. An untrusted `.clio-coder/settings.yaml` is ignored by design until `clio-coder config trust settings --hash <digest>`, but the only notice sat in the trailing Issues block, so a project `chat.retry.streamStallMs` looked like a setting that failed to apply.
+- Give the wait for a call's first token its own window, `chat.retry.firstTokenStallMs` (default 600000). One 180 s timer covered both the first token and mid-stream silence, although the setting is documented as measured from the last token received. A local llama-server that slept reloads in about 150 s and then prefills cold, so healthy turns were aborted and retried. `streamStallMs` still catches a stream that goes silent after it started, and re-arms at the first token.
+- Accept `clio-coder --autonomy <level>` for the interactive session. Only `clio-coder run` took the flag, so the supervised start that the WTF-P guide documents failed as an unknown global option. The flag seeds the same one-session override `/settings` uses and leaves `settings.yaml` untouched. Before a subcommand it is refused with the `run --autonomy` form named, because dropping a safety level silently would be worse. The top-level help now also lists `clio-coder mcp`.
+- Clear the remaining lint findings and split the web framework into its own chunk, which removes the oversized entry-chunk warning.
+
 ## 0.4.8 - 2026-09-12
 
 Clio Coder 0.4.8 strengthens the terminal and headless harness: settings take effect consistently, provider and usage records stay tied to the right request, and startup, reload and shutdown retain their cleanup guarantees. Start with `clio-coder configure`, then `clio-coder` for interactive work or `clio-coder run` for headless tasks. The optional web app and local PWA add another way to reach the same runtime; they do not replace the CLI, TUI or ACP.

package/README.md

@@ -73,11 +73,12 @@ setup, diagnostics, headless runs, and automation; `clio-coder --help` lists
 it. An optional local **browser app** over the same runtime is described under
 [Optional browser app](#optional-browser-app). The first session does not need it.
 
-**New in 0.4.8:** More reliable live settings, provider accounting and runtime
-cleanup, an npm-backed installer, and an optional web app with documentation
-generated from the Markdown guides. See the
-[changelog](CHANGELOG.md) for release details and [Install](#install) for source
-builds and other package managers.
+**New in 0.4.9:** File tools report bounded reads, atomic edits, and partial
+search results more precisely. Script runs retain streamed logs and provenance,
+and scientific verification exposes explicit tolerance and non-finite policies.
+A capability gateway adds data inspection and trusted local MCP alongside
+secondary tools. See the [changelog](CHANGELOG.md) for release details and
+[Install](#install) for source builds and other package managers.
 
 ## Built for scientific software
 
@@ -372,7 +373,7 @@ can also be installed with your package manager. See
 From source, the latest stable release uses the pinned pnpm workflow:
 
 ```bash
-git clone --branch v0.4.8 https://github.com/iowarp/clio-coder.git
+git clone --branch v0.4.9 https://github.com/iowarp/clio-coder.git
 cd clio-coder
 corepack enable pnpm
 pnpm run install:local

package/dist/{acp-JWPQZM2D.js → acp-ZWZCPS2A.js}

@@ -1,29 +1,29 @@
 import { createRequire as __clioCreateRequire } from "node:module"; const require = __clioCreateRequire(import.meta.url);
-import {
-  runClioCommand
-} from "./chunk-IILXVWJY.js";
 import {
   restoreStdout,
   takeOverStdout,
   writeRawStdout
 } from "./chunk-7WLRF2U5.js";
-import "./chunk-YKIIWURD.js";
-import "./chunk-PFZJMXIY.js";
+import {
+  runClioCommand
+} from "./chunk-KW6OJ7IY.js";
+import "./chunk-OA2GDACN.js";
+import "./chunk-IALGWTLO.js";
 import "./chunk-FXFVDPWY.js";
 import {
   printError
-} from "./chunk-ATB3Q7YO.js";
-import "./chunk-44U2OUSM.js";
+} from "./chunk-KIVFXGBM.js";
+import "./chunk-W72LLZAV.js";
 import "./chunk-X6FLVUM5.js";
-import "./chunk-PAQVETLA.js";
-import "./chunk-VNBICSS2.js";
-import "./chunk-DXVMLM3Z.js";
-import "./chunk-PGEFOTJB.js";
+import "./chunk-FPS4R2RN.js";
 import "./chunk-DVNAPPXU.js";
-import "./chunk-3XE4NRLF.js";
+import "./chunk-ZKJU55MX.js";
 import "./chunk-U2MSJ57E.js";
 import "./chunk-C27U2TYG.js";
+import "./chunk-ZKVMDNAN.js";
+import "./chunk-VNBICSS2.js";
 import "./chunk-B5GGDIHT.js";
+import "./chunk-DXVMLM3Z.js";
 import {
   MAX_TIMER_DELAY_MS
 } from "./chunk-6EXUUOSN.js";
@@ -127,4 +127,4 @@ async function runAcpCommand(args, options = {}) {
 export {
   runAcpCommand
 };
-//# sourceMappingURL=acp-JWPQZM2D.js.map
+//# sourceMappingURL=acp-ZWZCPS2A.js.map

package/dist/{agents-4GCDIRVX.js → agents-LYSOWZUE.js}

@@ -1,92 +1,93 @@
 import { createRequire as __clioCreateRequire } from "node:module"; const require = __clioCreateRequire(import.meta.url);
-import "./chunk-5UG6EZI3.js";
-import "./chunk-P4JS3MH5.js";
-import "./chunk-P7GTE4FX.js";
+import "./chunk-RDKX2PME.js";
+import "./chunk-LWJYOHT3.js";
+import "./chunk-XRECG65F.js";
 import {
   ConfigDomainModule,
   loadDomains
-} from "./chunk-2SXGG2IV.js";
-import "./chunk-Q32C6AWI.js";
-import "./chunk-PMUUAABD.js";
-import "./chunk-JLBVCROW.js";
+} from "./chunk-XJZEDCNT.js";
+import "./chunk-BMNVVKEW.js";
+import "./chunk-2DRRZ57Q.js";
 import {
   ensureClioState
-} from "./chunk-JIMWEYWO.js";
-import "./chunk-O2QJDRWP.js";
-import "./chunk-QH3ZTUOA.js";
-import "./chunk-LQTKDAUO.js";
-import {
-  SafetyDomainModule
-} from "./chunk-2ZWLMA3T.js";
-import "./chunk-YKIIWURD.js";
+} from "./chunk-EHZRAB4U.js";
 import "./chunk-QJMRYTCX.js";
-import "./chunk-GJBJHJNY.js";
-import "./chunk-PFZJMXIY.js";
+import "./chunk-AM6CEP2K.js";
+import "./chunk-PJI57EC6.js";
+import "./chunk-OA2GDACN.js";
+import "./chunk-JU6MAMRJ.js";
 import {
   AgentsDomainModule
-} from "./chunk-LZDLYSUN.js";
-import "./chunk-RFULVPBX.js";
-import "./chunk-ORRNGQDV.js";
-import "./chunk-OEMFEL26.js";
-import "./chunk-EXKUF426.js";
+} from "./chunk-5RTEFNBP.js";
+import "./chunk-WGRDABW7.js";
+import "./chunk-Y3M2T5RO.js";
+import "./chunk-7FBCRWVT.js";
 import "./chunk-DNCE23JJ.js";
 import "./chunk-YJCCMYYT.js";
-import "./chunk-7QQRPB2E.js";
-import "./chunk-6UJ7RDI7.js";
+import "./chunk-IALGWTLO.js";
 import {
   printError
-} from "./chunk-ATB3Q7YO.js";
-import "./chunk-44U2OUSM.js";
-import "./chunk-MUXNDNMZ.js";
-import "./chunk-RAUOKUZV.js";
-import "./chunk-X6FLVUM5.js";
-import "./chunk-5C2OQHLR.js";
-import "./chunk-B5ZTR6KZ.js";
-import "./chunk-TOPICHGR.js";
-import "./chunk-B6UM3OZC.js";
-import "./chunk-MYI32N4R.js";
+} from "./chunk-KIVFXGBM.js";
+import "./chunk-W72LLZAV.js";
+import "./chunk-XCUDZQLX.js";
+import "./chunk-K2BLQC5E.js";
+import "./chunk-QH3ZTUOA.js";
+import {
+  SafetyDomainModule
+} from "./chunk-GREYLTZ5.js";
+import "./chunk-PTFISXQO.js";
+import "./chunk-LQTKDAUO.js";
+import "./chunk-7QQRPB2E.js";
+import "./chunk-6UJ7RDI7.js";
+import "./chunk-AY4XE6GN.js";
+import "./chunk-2JBZYUPY.js";
+import "./chunk-CTGZCEI6.js";
+import "./chunk-RL7LJYN4.js";
 import "./chunk-W5RM7YAH.js";
-import "./chunk-PAQVETLA.js";
-import "./chunk-VNBICSS2.js";
-import "./chunk-DXVMLM3Z.js";
+import "./chunk-IC7JXLOM.js";
+import "./chunk-X6FLVUM5.js";
 import {
   isUserVisibleAgent
-} from "./chunk-ARRUMZ7X.js";
+} from "./chunk-I47EJPYL.js";
 import "./chunk-XW2UZICE.js";
-import "./chunk-PGEFOTJB.js";
+import "./chunk-FPS4R2RN.js";
 import "./chunk-DVNAPPXU.js";
 import "./chunk-5EQO5NWP.js";
-import "./chunk-YXFKLMX2.js";
-import "./chunk-E2NSPYLC.js";
+import "./chunk-H2WSCZZT.js";
+import "./chunk-SQBT46OF.js";
+import "./chunk-KQ6IDQIB.js";
+import "./chunk-H72DCH3E.js";
+import "./chunk-2KUBKL63.js";
+import "./chunk-MYI32N4R.js";
 import "./chunk-R2P2U3ZS.js";
 import "./chunk-NTTS3O53.js";
-import "./chunk-KQ6IDQIB.js";
 import "./chunk-M4KFUXS7.js";
-import "./chunk-WLHX3MM5.js";
-import "./chunk-3XE4NRLF.js";
+import "./chunk-V4XJWDHR.js";
+import "./chunk-ZKJU55MX.js";
 import "./chunk-U2MSJ57E.js";
 import "./chunk-C27U2TYG.js";
+import "./chunk-ZKVMDNAN.js";
+import "./chunk-VNBICSS2.js";
 import "./chunk-B5GGDIHT.js";
-import "./chunk-GJ24ODAX.js";
+import "./chunk-SRCEQKQS.js";
+import "./chunk-DXVMLM3Z.js";
+import "./chunk-XTQ7MEJG.js";
 import "./chunk-LTR5QCLS.js";
 import "./chunk-6EXUUOSN.js";
 import "./chunk-ZTNFYMIO.js";
-import "./chunk-6R5MBXBJ.js";
+import "./chunk-NBPA5QM6.js";
 import "./chunk-EM2WNQS2.js";
-import "./chunk-36XSBPXL.js";
-import "./chunk-UHW5V7HC.js";
 import "./chunk-DVJL77SO.js";
+import "./chunk-3RDHGNU7.js";
+import "./chunk-UHW5V7HC.js";
 import "./chunk-KMF54VH3.js";
 import "./chunk-SER7RRAE.js";
 import "./chunk-GH5ZR6JP.js";
 import "./chunk-TK2BMCBZ.js";
-import "./chunk-XCUDZQLX.js";
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 import "./chunk-CTTI7G3T.js";
 import "./chunk-ZZFWWYLX.js";
 import "./chunk-GD55RTIW.js";
 import "./chunk-E3LEPLQ2.js";
-import "./chunk-SRCEQKQS.js";
 import {
   init_esm_shims
 } from "./chunk-ECBHH7LU.js";
@@ -146,4 +147,4 @@ function renderLine(spec) {
 export {
   runAgentsCommand
 };
-//# sourceMappingURL=agents-4GCDIRVX.js.map
+//# sourceMappingURL=agents-LYSOWZUE.js.map