Feat/skill management#24
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Bridge dsagt's skill system into agent-native discovery and add a searchable catalog of installable skills from external GitHub repos. Two tiers: - Catalog — external Agent-Skills repos (default: K-Dense scientific, 140+) cloned + indexed into per-source `skills_catalog__<slug>` KB collections. Searchable via search_skills, never loaded into the agent's context. - Installed — a chosen skill copied into <project>/skills/ and mirrored into .claude/skills/ for Claude Code's native discovery. Changes: - commands/skills_catalog.py: shallow-clone cache, recursive SKILL.md discovery, per-source indexing (idempotent re-sync via drop+rebuild), find/install. Known sources: scientific, anthropic, antigravity, composio. - MCP tools: install_skill + catalog-spanning search_skills (registry); add_skill_source / list_skill_sources (knowledge). Added to auto-allow. - agents/base._mirror_skills_to + ClaudeSetup hook: manifest-gated mirror into .claude/skills/ (never clobbers user skills; reaps stale entries; trims >1536-char descriptions in the copy only). - Bundled skill-creator meta-skill (Anthropic template + condensed spec). - CLI: dsagt skills sync/add/list/search. - Config: skills block (sources/populate_native/populate_catalog), backfilled for old configs; setup-kb syncs the default catalog (--no-skill-catalog to skip); reserve .skill_sources; kb_from_config. - dsagt_instructions.md: two-tier guidance (native vs catalog/install). - use_cases/isaac_skills_demo: runnable mock of the isaac_vasp workflow exercising the full flow with tiny mock VASP data. Tests: test_skills_catalog.py + config/server-routing additions (201 passed, 13 skipped); black + ruff clean. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
First-pass vetting of use_cases/isaac_skills_demo against the real K-Dense catalog surfaced one bug: `dsagt skills add <proj> <source>` synced + indexed the catalog but never wrote the source into dsagt_config.yaml, so a later config-driven `dsagt skills sync` would forget it. Only the `add_skill_source` MCP tool persisted. - Move the persist logic into a shared `persist_source_to_config` helper in skills_catalog.py; call it from both the CLI add-source path and the knowledge-server `add_skill_source` handler (removes the duplicated `_persist_skill_source`). - Regression test for the helper (append + dedupe + missing-config no-op). - Add use_cases/isaac_skills_demo/PROMPTS.md: the 8-prompt hand-pass script plus first-pass results (init/mirror, 146-skill sync, search, install pymatgen, native re-mirror, add anthropic all verified). Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
The isaac_skills_demo rebuild path (rm + init) left the external catalog empty because a fresh `init` copies only the shared KB, while the catalog is project-scoped. The agent's search_skills then correctly returned no catalog hits. Add the required `dsagt skills sync` step to the rebuild block, a pre-launch catalog check, and a note on the global setup-kb alternative. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
An empty/unsynced external skill catalog was indistinguishable from a genuine no-match, forcing the agent through a multi-step discovery dance and a misleading "skill unusable until restart" message. - search_skills: when no catalog is synced, say so and point at list_skill_sources / add_skill_source instead of a bare no-match - list_skill_sources: flag each known source synced/available with its indexed count, rather than two parallel lists to cross-reference - install_skill: state the skill is usable this session immediately; restart only enables hands-free native auto-invocation - dsagt_instructions: document the catalog as opt-in and the list_skill_sources -> add_skill_source -> search_skills -> install flow Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
Bump to 0.2.0 and make dsagt.__version__ the single source of truth — pyproject reads it via setuptools dynamic metadata, so future bumps touch one line. Add CHANGELOG (Keep a Changelog format). Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
- README/docs: document the non-developer install (pip install git+https://github.com/AI-ModCon/dsagt.git into any 3.12/3.13 env); note uv is dev/CI-only and conda/venv both work - de-duplicate the supported-agents table and install block via mkdocs-include-markdown so docs/index.md pulls them from the README - correct the Python prerequisite to 3.12/3.13 - cli.md: drop the uv-sync-specific install assumption - docs CI builds with the locked docs dependency group via uv Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
…Catalog + keyword fallback
Collapse the two MCP servers (dsagt-registry-server + dsagt-knowledge-server)
into a single dsagt-server backed by one shared KnowledgeBase, and finish the
skills-discovery refactor from design-notes/genesis-skills-comparison.md §10 and
skills-catalog-server-merge.md.
Server merge
- New commands/dsagt_server.py: create_dsagt_server composes both modules'
(tools, handlers) under one Server("dsagt") with a type-dispatched call_tool
(registry str passthrough + knowledge dict->json + error wrap); one shared-KB
main() with the cross-backend guard living once in _build_kb_from_config.
- registry_server / knowledge_server keep create_*_server as thin test-facing
wrappers via extracted _registry_tools_and_handlers / _knowledge_tools_and_handlers;
their standalone main()s + entry points are removed.
- pyproject: dsagt-registry-server + dsagt-knowledge-server -> dsagt-server.
- Per-agent MCP config collapsed to one "dsagt" entry across claude/goose/codex/
cline/roo/opencode (+ base helpers, info.py span buckets).
- Compat is rebuild-not-migrate: re-run `dsagt start` to regenerate config
(README upgrade note + cline .cline-data caveat). No migration shims.
Skills discovery
- New SkillsCatalog (commands/skills_catalog.py) owns the catalog data plane
(sync/install/search/list_sources + ChromaDB-vs-keyword backend selection);
SkillRouter is now a thin render/MCP facade over it.
- New skill_keyword.py: Genesis-faithful token-overlap scorer (no-embedder
fallback). skill_discovery.py: stateless SkillRouter.
- Catalog-only search + frontmatter-only indexing; removed the dead
skills-collection indexing (SkillRegistry + setup_core_kb bundled skills).
- Struck the stale bundled datacard-generator skill (now via `dsagt skills add
<project> genesis`); skill-creator is the only bundled skill.
Docs/diagram
- Architecture figure: one MCP box spanning Knowledge + Registry, "Server"
dropped from both labels, Skills -> Skills Catalog; regenerated PNGs.
- README/docs/design-notes updated.
Tests: new test_dsagt_server.py + test_skill_discovery.py; config-shape, info,
and smoke-test assertions updated to the single-server shape. 338 passed /
13 skipped across affected suites; ruff + black clean on changed files.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
…overy Bump to 0.3.0 (breaking: the registry/knowledge MCP servers merge into one dsagt-server; the old console scripts are removed). CHANGELOG documents the motivation and a rebuild-not-migrate upgrade note; README version refs bumped. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
- Add the skill-routing diagram (assets/skills-routing.png) to tools-skills.md with a "Skill discovery architecture" section motivating the two-tier (catalog vs native) split, catalog-only search, the keyword fallback, the single SkillRouter entry point, and per-source federation/provenance. - Sweep README + docs for the old two-server model: mcp-servers, architecture, cli, developer, quickstart, knowledge-base now describe one dsagt-server. - Fix stale skill-indexing language: bundled/installed skills are auto- discovered natively (not indexed); setup-kb rebuilds Tool Specs only; the KB collection tables list "Skills Catalog" (external, per-source) instead of a bundled "Skills" collection. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
The README/docs documented `dsagt --version` but the CLI had no such flag (argparse errored). Wire it from dsagt.__version__ so it reports the release the docs claim. Found while vetting the isaac_skills_demo walkthrough. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
…source name clashes When the same skill name exists in more than one synced source (the clone cache is machine-global, so this happens even across projects), the install guard now resolves a source-qualified '<slug>/<skill>' name instead of dead- ending. find_catalog_skill parses the '<slug>/' prefix and scopes the search; install_skill (MCP) and 'dsagt skills add' inherit it. The CLI 'add' routes a '<synced-slug>/<skill>' target to install (not a clone) and now prints a clean error instead of a traceback on an ambiguous bare name. The ambiguity message points at the qualified form, which actually works now. Found while vetting the isaac_skills_demo walkthrough. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
…r 0.3.0 Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
…package; consolidate skill modules into skills.py The single dsagt-server now lives in src/dsagt/mcp/, composed from per-concern tool modules behind one dispatch shell: - mcp/server.py — composition, main(), shared build_dispatch_server + KB startup - mcp/registry_tools.py / knowledge_tools.py / memory_tools.py / skill_tools.py This replaces the registry_server / knowledge_server / dsagt_server trio and moves importable logic out of commands/ (which is for entry points). Entry point repointed to dsagt.mcp.server:main; agents are unchanged (same `dsagt-server`). Skill discovery is consolidated into one module src/dsagt/skills.py — the catalog data plane (SkillsCatalog), the SkillRouter render facade, and the Genesis-derived keyword scorer (was skill_keyword + skill_discovery + commands/skills_catalog). install_skill now returns a terse confirmation (the install→use→restart model already lives in the agent instructions). Remove dead src/session.py. Migrate tests to the new layout (new test_memory_tools / test_skill_tools; server-startup reworked to fast, network-free entry-point checks; memory + kb_search tests rehomed). Update CLAUDE.md and docs/mcp-servers.md to the merged-server / four-concern shape. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
…ntmatter Third-party catalogs (e.g. Genesis) ship SKILL.md files whose unquoted `description` contains a colon (`…readiness levels: Level 1…`), which strict YAML rejects — so _parse_frontmatter raised and the skill was silently dropped from indexing, search, and install. Genesis's `generating-datacards` (datacard-generator) was one such casualty. _parse_frontmatter now falls back to a lenient flat key:value parse on YAML error, recovering name/description/tags. dsagt-authored specs are valid YAML, so the fallback never fires for them. Adds TestLenientFrontmatter. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
Consolidate the branch into one 0.2.0 release: a single CHANGELOG entry (external skill catalogs incl. the Genesis integration, native discovery, catalog-only search + keyword fallback, license/PROVENANCE capture, server merge) replacing the interim 0.2.0/0.3.0 entries; version set to 0.2.0 (one minor bump from master's 0.1.0). README/architecture diagram refreshed. Add two skill-management use cases: - isaac_skills_demo — agent-led arc (what we have → find more → sync → install → create) that authors a vasp-to-isaac converter parsing with real pymatgen. - genesis_skills — pull Genesis curation skills, ingest domain into the KB, and generate a datacard for a finished dataset. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
Recover observability and episodic memory without the LiteLLM proxy, by reading each agent's own on-disk session transcript instead of intercepting LLM traffic — no proxy, no credentials, serverless trace store. Trace pipeline (Phase 2), all in one src/dsagt/traces.py: - `Trace` — the canonical session form as nested dicts (a list of span dicts + compose/query/to_exchanges methods; the span/message/block shapes have a single home in Trace's add_* methods). - `Reader`/`Translator` ABCs with one subclass per agent (claude/codex/goose/ opencode/cline); codex/goose/opencode/cline share the Translator turn- template, claude is bespoke, claude+codex share JsonlReader. - `TraceCollector` — the in-session heartbeat: read → translate → hand the Trace to its consumers, each with its own ack set for idempotency. - `MLflowSink` (observability) consumes Trace + dict spans directly. Episodic memory (Phase 3, opt-in via `dsagt init --episodic`): - `memory.MemoryExtractor` — a TraceCollector consumer: Tier-0 mechanical chunk+tag+embed always; Tier-1 distillation via `judge.LocalJudge` (Qwen2.5-1.5B GGUF, GBNF-grammar JSON), degrading to Tier-0 on failure. - Recency-weighted retrieval over session_memory (episodic.recency_half_life_days). - `judge.py` — Judge.create → LocalJudge (default) / APIJudge; llama-cpp-python added to core, pinned to an integrity-verified CPU wheel. Tool-use indexing: - `provenance.ToolUseIndexer` — incremental, idempotent embedding of dsagt-run records into the tool_use collection on the heartbeat + before reconstruct_pipeline (fixes the prior re-index-everything duplicate bug). Removed: the LiteLLM proxy (commands/proxy_server.py, test_proxy_callback, proxy_walkthrough) and the roo agent. Docs (README, docs/ site, CHANGELOG) updated to the post-proxy, serverless, episodic-enabled reality. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
…r MCP Reserve "tool"/"tools" for the MCP + agent sense; registered CLI executables the agent runs via dsagt-run are now "codes" throughout. - Registry: <project>/tools/ → codes/ (+ codes/scripts/), ToolRegistry → CodeRegistry, save_tool_spec → save_code_spec, search_registry takes code_name, dsagt-run --tool → --code, list_tools/get_tool → list_codes/get_code. - Collections/spans: tools → codes, tool_use → code_use, tool.execute → code.execute; provenance/registry metadata tool_name → code_name. Kept tool_name for session_memory (agent tool calls); kb_search now accepts both code_name and tool_name. - src/dsagt/tools/ → src/dsagt/codes/, run_tool.py → run_code.py (+ package-data, dsagt-run entry point, bundled scan_directory). - Agent instructions, CLAUDE.md, README, and all docs updated to the convention. Kept the Anthropic tool_use block type and the MCP SDK @server.list_tools() decorator (both the reserved sense). Docs also: fixed staleness (dropped Roo, the removed mlflow-autolog hook, the removed LLM judge), trimmed implementation-detail TMI and negative framing, simplified jargon (provisioning → setup, dropped "layer"). Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
…nit` - Restructure the docs into one page per capability, each ending with a hands-on "Try it" walkthrough and a pointer to the use cases: provenance (code registry + dsagt-run + reconstruction), knowledge-base (domain-knowledge cataloging + hybrid vector search + shared-store note), skills, memory, observability. Split the old codes-&-skills page, move memory + execution-record content out of knowledge-base, and regroup the mkdocs nav under a "Capabilities" section. - Docs now lead with the interactive `dsagt init` menu; every walkthrough uses bare `dsagt init` + `dsagt start`. The pre-menu flags (positional name, --agent, --location, --include/--exclude, --episodic) are documented as deprecated backcompat only in the CLI reference and README. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
# Conflicts: # README.md # pyproject.toml
The handler now always forwards where_document (the regex/contains document-content filter) to kb.search; the three call-signature assertions predated that argument. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
…flow deprecation - http_request was the only MCP tool with no handler-level test; add success/method-forwarding/transport-error cases with a mocked httpx.AsyncClient. - test_running_job held its worker in 'running' with a real time.sleep(10) that asyncio.run joined at loop shutdown; gate on a threading.Event released once the test observes the running state. - test_install_skill_routes_and_reports_missing built a real local-embedding KnowledgeBase it never used (the install path builds its own SkillRouter) and scanned the machine-global skill_sources cache; use a mock KB and point SKILL_SOURCES_DIR at a tmp dir. - mlflow.search_traces(experiment_ids=...) is deprecated in favor of locations= (FutureWarning under mlflow 3.11); switch the five call sites. Suite: 621 passed, 0 warnings, ~31s (was ~56s). Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
…Tel/csvtool era removed Smoke test now runs two back-to-back dsagt start sessions and asserts 15 artifacts instead of 7: - Agent LLM-trace recovery is a HARD assertion (was informational, waiting on 'Phase 2' — the trace pipeline landed). The OTel block and its agent_otel_support helper are removed from source entirely (function, __all__, otel_payload_support class vars, docstring matrix) — the smoke script was the last consumer. - greet.py replaces the abandoned-csvtool fixture as a registerable AND executable code (stdlib-only, documented GRT-42 error code); the knowledge/ docs describe it, so registration, execution, provenance, and retrieval all reference one consistent tool. Execution is proven by greet's actual stdout in the trace_archive record; retrieval by the agent answering GRT-42 (only present in the ingested docs). - New coverage: skill catalog search+install, episodic memory (--episodic init, session_memory collection), code_use indexing, reconstruct_pipeline prompt, state.yaml session log + trace_source, dsagt info, and session 2's cross-session recall + startup catch-up. - ExplicitMemory now roots at <project>/.dsagt/ as CLAUDE.md and the user docs document (the code was the outlier at project root). - Knowledge-ingest assert fixed to chroma_ids.json — route.json marks routed external collections, which ingest never creates. - Serverless staleness: run.sh header, cli.py 'MLflow ports' docstring. - manual_runs/ walkthroughs moved to tests/manual_walkthroughs/ (they document the dropped roo agent — kept off the docs site until refreshed); developer.md link updated. Verified end-to-end with --agent claude: 15/15 checks pass (the one first-run failure was the stale route.json assert, re-verified against the run's artifacts after the fix). Unit suite: 621 passed. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
…ening from the 4-agent sweep Running the smoke test across codex/goose/cline/opencode surfaced one product bug and three harness issues: - CodexReader scanned the global ~/.codex/sessions/, but DSAGT always launches codex with CODEX_HOME=<project>/.codex-data (its MCP config lives there), so rollouts land project-local and the live trace pipeline collected NOTHING for codex — no MLflow traces, no episodic memory, no trace_source stamp for crash catch-up. Default the reader to <project>/.codex-data/sessions. Verified end-to-end: codex smoke now 15/15. - The smoke agent-trace check masked that bug: its service.name span heuristic counted internal DSAGT spans lacking the attribute as agent traces. Count MLflowSink's positive dsagt.trace_id trace-metadata marker instead (validated per-store: claude 1, goose 5, opencode 1, broken-codex 0). - cline: dsagt start --script hard-errors by design (agents/cline.py), so the harness SKIPs cline with that explanation instead of 15 red checks. - greet execution: goose put 'Ahoy' in both arg slots and opencode ran greet through bare bash (bypassing dsagt-run) — the prompt now names both arguments and steers to the spec's dsagt-run command, and the assert matches the greeting prefix only. Opencode passes with the steered prompt. Sweep verdicts: claude 15/15, codex 15/15, opencode 15/15, goose 14/15→pass (both changed checks verified against its artifacts), cline SKIP. Unit suite: 621 passed. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Agents routinely sidestepped MCP-dispatched execution with their own bash tools; dsagt-run inside the stored command makes that path harmless. Capture the rationale where the wrapping code lives. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
…tive skills Registered codes move from flat codes/<name>.md to skill-standard directories (codes/<name>/SKILL.md + per-code scripts/), making each code a self-contained, portable dir structurally identical to an installed skill. Because codes now share the skill envelope, setup_skills mirrors them into the agent's native skills dir unchanged — native discovery puts the exact dsagt-run command in context at invocation time, a second discovery path (alongside search_registry) aimed at the from-memory command-reconstruction failure mode observed with opencode. The agent-facing MCP surface is unchanged. - Code names constrained to the skill charset (lowercase-hyphen); save_code_spec validates with an actionable error. Bundled code renamed scan_directory → scan-directory (python module unchanged). - SKILL.md body leads with the exact wrapped command + the copy-byte-for-byte instruction — what native discovery injects. - Mirror order: codes first, skills last — a deliberately installed instruction skill wins a name collision with a code. - dsagt start again refreshes the dynamic agent record (MCP config + native mirror, all idempotent) — the refresh had been dropped from _cmd_start, silently breaking install_skill's 'available after the next dsagt start' promise; restored, so mid-session-registered codes and installed skills mirror at the next start. - opencode gains its missing native_skills_dir (.agents/skills, the AGENTS.md-convention dir codex/goose already use) — it was the one agent with no native mirror at all. - Smoke test asserts both native mirrors (bundled code at session 1's start, mid-session-registered greet at session 2's). Verified end-to-end: smoke sweep PASS 4/4 (claude, codex, goose, opencode; cline SKIPs by design). Unit suite: 624 passed. Known issue (pre-existing, surfaced by a parallel sweep): concurrent dsagt init runs race on projects.yaml registration — smoke-test --all can clobber project registrations; needs a file lock. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
- dsagt init hard-failed for cline without ANTHROPIC_API_KEY / ANTHROPIC_MODEL in the shell — a batch-mode-era requirement, though cline batch is unconditionally unsupported. Worse, running `cline auth -p anthropic` from scavenged env vars can clobber an existing provider integration (e.g. an OpenAI subscription login). BYOA: the user configures cline before pointing dsagt at it; dsagt writes only the MCP config. credential_env_vars/hints dropped. - cline 3.x moved --config to a global option (must precede the subcommand) and made `mcp add` open an interactive wizard without --yes; both fixed (probe-verified against cline 3.0.34). Verified: credential-less `dsagt init --agent cline` completes — instructions written, MCP server registered + env-patched, 2 skills mirrored natively. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
…ctions agent-card.md described the pre-0.2.0 architecture (two MCP servers, LiteLLM proxy, OTel/OTLP, setup-kb/mlflow/memory/stop commands, Roo Code, dsagt_config.yaml, faiss). Rewritten in the same card format: single dsagt-server with all 20 tools enumerated by concern, serverless sqlite MLflow store, BYOA auth, transcript trace pipeline, codes as skill-standard dirs with native mirroring, current agents/deps/CLI, and a skill_discovery capability replacing the no-longer-bundled datacard-generator. dsagt_instructions.md fixes: the 'scientific' skill source doesn't exist (→ k-dense-ai); codes/scripts/ → codes/<name>/scripts/; code-name charset rule beside the save_code_spec guidance; and a note that registered codes appear among native skills, whose SKILL.md opens with the exact command — same verbatim-executable rule as section 1b. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
…l hint machinery
Extends the cline decision to every agent: the user configures and
authenticates their agent (shell env vars, subscription logins) BEFORE
pointing dsagt at it. dsagt neither hints, warns, nor troubleshoots.
Removed: credential_env_vars / credential_hints class vars on all five
setups, byoa_env_hints(), and the launch-time 'agent will use
preconfigured env vars' transparency note (+ their 18 tests).
Kept (functional, not troubleshooting): opencode's {env:VAR} provider
interpolation in opencode.json, codex's auth.json propagation into the
per-project CODEX_HOME, and batch-mode requirements that genuinely need
an env value (OPENCODE_MODEL for opencode run -m).
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
python -m execution is the only machine-independent executable for package-shipped code, and module paths can't contain the hyphen the skill-standard dir name requires — so bundled implementation modules sit beside their spec dirs, unlike project codes whose scripts are self-contained in codes/<name>/scripts/. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
…l whitelist Re-verified against cline 3.0.34: batch runs fine (act mode, subscription auth honored), but the headless CLI session path never loads MCP servers — a probe session with a registered dsagt entry exposed zero MCP tools. Also verified: cline auth state rides with its config dir, so ANY per-project --config/CLINE_DIR isolation loses a subscription login; subscription users need a single global MCP entry (the server is cwd-self-sufficient). run_script error + smoke SKIP updated to the current rationale; re-probe on cline upgrades. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
…never bridge Deeper probes (spawn watcher, MCP-child cwd/env probe, tool-inventory enumeration): headless cline spawns registered MCP servers with cwd = session dir and full shell env, and dsagt-server answers the initialize handshake in ~1.6s — but the session's model toolset contains only cline built-ins + team tools, zero MCP entries. Also pinpointed the auth coupling: providers.json (subscription/OAuth creds) lives inside the settings dir, which is why any --config isolation goes Unauthorized. A global MCP entry is not viable either: it makes every cline session everywhere spawn dsagt-server. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
…e, one format Parity: every available code — bundled or agent-registered — now lives in <project>/codes/<name>/ as a self-contained skill-standard dir. ensure_bundled_copies() runs at dsagt init (never clobbers an existing dir; re-init after upgrade refreshes untouched copies). This dissolves the bundled/project two-layer merge in CodeRegistry (single glob, no source_tools_dir seam) and the scan_directory.py placement asymmetry: the script moves inside scan-directory/scripts/ and the executable becomes an ordinary project-relative path instead of python -m. reindex_all removed (no production caller). Verified: claude smoke 18/18 with scan-directory executing via the project-relative path. Unit suite: 607 passed. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
…bal auth + settings untouched Cline 3.x resolves its MCP settings file and providers.json (auth) through INDEPENDENT env overrides. Setting CLINE_MCP_SETTINGS_PATH to <project>/.cline-data/cline_mcp_settings.json in runtime_env gives all three at once (verified live): per-project dsagt server spawns, the user's subscription/codex auth keeps working, and the global mcpServers list stays empty. write_dynamic now hand-writes that file directly (the 'only cline mcp add is loaded' behavior is gone in 3.x; verified a hand-written file loads) with the env block in transport.env — no cline binary needed at init, no add+patch dance, preserves user-added entries. The auth-clobbering CLINE_DIR runtime isolation is dropped. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Non-invasive correctness pass across the use-case walkthroughs (comb-flow-uni left untouched by request). Each demo gets an 'Estimated time' header with an honest runtime + data/credential gate. Uniform staleness fixed: - tool→code terminology; save_tool_spec→save_code_spec; tools/<x>.md→ codes/<x>/SKILL.md (registry is skill-standard dirs now). - removed commands dropped: dsagt mlflow / dsagt stop / dsagt setup-kb / dsagt skills — replaced with the current init/start/info surface or the MCP-tool equivalents. - serverless observability: deleted the tokamak OTEL_* export block and 'dsagt mlflow' server start; point at sqlite:///<project>/mlflow.db and the 'mlflow ui --backend-store-uri' view. - BYOA: dropped 'set your API keys in dsagt_config.yaml' edits; agents are pre-authenticated. Config path corrected to .dsagt/config.yaml. - isaac_skills_demo: 'scientific' skill source → 'k-dense-ai' (the real KNOWN_SOURCES alias); setup uses 'dsagt init --exclude genesis'. Per-folder: - isaac_vasp: rewrote the 12-line stub into a real ~15-min walkthrough that registers the bundled NEB converter as a code and runs it via dsagt-run on the vendored fixture data; fixed a dangling script ref (ase_slab_db_to_isaac → ase_db_to_isaac) in the skill. - tokamak_stability: README + AGENTS.md + m3dc1-skill swept (filenames like m3dc1_tools.py preserved). - .gitignore: guard mlflow.db + mlruns/ so session trace dumps never land in git again. Deferred (flagged, not done): externalizing isaac_vasp's 32 MB OUTCAR fixtures — the pymatgen source path 404s and I couldn't verify a fetch URL without risking a broken demo. comb-flow-uni left entirely as-is. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
A 12-line plan outline fully superseded by isolate_demo.md (same walkthrough, more detail). Referenced nowhere in README/docs. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
… transcript - docs/use-cases/*: 'tool registration' → 'code registration' (index synced with README), '**Tools:**' header labels → '**Codes:**', and the vasp/cryoem overviews reworded (registers codes, not tools; ISAAC record not database). - Removed use_cases/microbial_isolates/isolate_session.txt — a personal scratch transcript with hardcoded paths and the dead two-server launch commands, referenced nowhere; same class as the demoplan.md already removed. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
csvkit was dropped as a dependency, but the README/docs quickstart still told users to register csvkit codes (csvcut/csvstat/...) — following it failed at that step. Replace with a bundled, stdlib-only fixture (tests/smoke_test/csv_summary.py: csv + statistics, no install) that the agent registers and runs on samples.csv — the same self-contained pattern the smoke test uses for greet.py. Its null-count output surfaces the empty status/timestamp cells, which is the exact fact the quickstart's explicit-memory step stores and recalls (previously asserted out of nowhere). - README.md + docs/quickstart.md: steps 2 & 4 + capability tables. - docs/provenance.md: the worked example spec and 'Try it' flow, and the example frontmatter updated to the current executable/parameters shape. - tests/test_csv_summary_fixture.py: deterministic guard on the fixture's columns / null-columns / numeric-stats so it can't drift from the docs. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
MCP-server traces had two hygiene problems (analyzed from a real store): 1. Orphaned background spans. The dispatch shell tags each tool-call root dsagt.source=<category>, but off-thread work (the heartbeat's CodeUseIndexer, the startup catch-up) ran outside any trace, so its kb.add_entries/kb.embed opened as untagged top-level traces — landing in the 'unknown' bucket and detached from the executions they index. Fix: CodeUseIndexer.tick_traced() wraps indexing in a dsagt.source=code_use root on the worker thread; heartbeat + startup catch-up use it (raw tick() stays for reconstruct_pipeline, which already runs under a registry root). 2. Episodic noise. Per-turn memory.extract shared dsagt.source=memory with the user-facing kb_remember/kb_get_memories. Retagged dsagt.source=episodic so internal embedding filters apart. dsagt info: recognizes episodic/code_use; adds an Agent turns vs Internal/debug headline split (unknown counts as internal, not agent). New: dsagt traces <project> — a frictionless MLflow viewer. Runs catch-up first (flushes the deferred last turn an ungraceful exit leaves unlogged), deep-links to the experiment's Traces tab (DSAGT writes traces not runs, so the default Runs view looks empty), and launches foreground + quiet (--workers 1, PYTHONWARNINGS=ignore) — no managed daemon, so the store stays serverless and there's no dsagt stop to add. Verified end-to-end: a fresh smoke run's store has 0 untagged orphans (was 2) with code_use + episodic present and every trace attributable. Suite: 617 passed (+9). Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
…start messaging install_skill / save_skill / save_code_spec now run the same idempotent native-skills mirror that init/start run (agents.refresh_native_skills), so .claude/skills/ is current the moment the files land — the next session auto-discovers them however the agent is launched, with no dependency on `dsagt start` (whose mirror remains as a backstop for hand-dropped skill dirs). Reword every message the agent takes its framing from (tool descriptions, dsagt_instructions.md, skill-creator's confirm step) to present installs as complete and immediately usable — the agent reads the SKILL.md this session (all native invocation does) and must not tell the user a restart is needed. Mid-session native *listing* remains agent-side behavior (platforms enumerate skills at session startup). Also drops a stale "no API key" clause from the README embedder line. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Setup → prompt dialogue → post-conditions: the mid-walkthrough shell checks move to one consolidated post-conditions block, so the user isn't bouncing to a terminal after every step. The two catalog searches merge into one conjoined prompt (verified against the live Genesis catalog: the keyword scorer ranks croissant-validator #1 and generating-datacards #3 of 74, so both surface from a single search). Design-history rationale and over-explaining parentheticals removed. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
The word people reach for when they want the MLflow viewer. Rewritten pre-parse (only the command slot — a project named "mlflow" is untouched) so argparse and --help only ever know `traces`; deliberately absent from the docs. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Condense [Unreleased] to under a page: keep the trace-pipeline / episodic entries (terminology fixed to code_use / code.execute, which the tools→codes rename missed here), add the work since — dsagt traces, dsagt.source span tagging, the codes rename, skill-envelope codes, install-time native mirroring, pre-authenticated agents, cline/codex fixes, docs restructure, new use cases. Dropped the stale 23→21 tool count. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
…older The "Try it" ingest prompt referenced a knowledge/ folder nothing creates; point it at <your-docs-folder> with a lead-in saying what to substitute. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
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Skills discovery feature and better skills management relying on agent native skills usage. Merged mcp servers to deal with communication between two servers issue. Updated use cases and docs.