Baseline v35

docs/diagram1_three_contexts.md

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+# diagram1_three_contexts
+
+```mermaid
+flowchart TB
+    classDef llm fill:#e3f2fd,stroke:#1565c0,stroke-width:2px,color:#000
+    classDef human fill:#fff3e0,stroke:#e65100,color:#000
+    classDef tool fill:#f1f8e9,stroke:#33691e,color:#000
+    classDef delta fill:#fce4ec,stroke:#ad1457,stroke-dasharray:4 3,color:#000
+
+    Thesis["<b>Today</b>: LLMs inform humans &nbsp;&nbsp;━━ 6-month step ━━▶&nbsp;&nbsp; <b>Tomorrow</b>: LLMs act within workflows"]:::delta
+
+    subgraph P1["① Real-time bot — Mattermost"]
+        direction TB
+        U1["ePIC users"]:::human
+        B1["AI bot<br/>Haiku · cross-session memory<br/>context harness"]:::llm
+        O1["Q&A, diagnostics, on-the-fly analysis"]
+        U1 --> B1 --> O1 --> U1
+    end
+
+    subgraph P2["② Research orchestrator — corun-ai"]
+        direction TB
+        U2["Expert evaluators<br/>(production, user learning)"]:::human
+        S2["Scheduler<br/>model × sysprompt × MCP set<br/>config compare & annotate"]
+        B2["Long-latency worker<br/>Opus / Sonnet / Gemini / Gemma<br/>minutes–tens of minutes"]:::llm
+        O2["Deep research entry<br/>(e.g. Perlmutter performance)"]
+        U2 --> S2 --> B2 --> O2 --> U2
+    end
+
+    subgraph P3["③ Active workflow orchestrator — swf-testbed"]
+        direction TB
+        U3["Testbed users"]:::human
+        B3["LLM orchestrator<br/>launch · run · monitor<br/>assess · summarize"]:::llm
+        W3["Hybrid workflow<br/>LLM steps ⇄ deterministic agents<br/>DAQ sim → PanDA workers"]
+        O3["Completed run + summary"]
+        U3 --> B3 --> W3 --> B3
+        W3 --> O3 --> U3
+    end
+
+    subgraph MCP["Shared MCP tool ecosystem"]
+        direction LR
+        IH["<b>In-house</b><br/>AskPanDA · PanDA Monitor · Streaming Workflow"]:::tool
+        AD["<b>Adopted</b><br/>Rucio · XRootD · uproot · LXR · GitHub · Zenodo"]:::tool
+    end
+
+    Thesis -.-> P1
+    Thesis -.-> P2
+    Thesis -.-> P3
+    P1 --> MCP
+    P2 --> MCP
+    P3 --> MCP
+```

docs/diagram1_three_contexts.mmd

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+flowchart TB
+    classDef llm fill:#e3f2fd,stroke:#1565c0,stroke-width:2px,color:#000
+    classDef human fill:#fff3e0,stroke:#e65100,color:#000
+    classDef tool fill:#f1f8e9,stroke:#33691e,color:#000
+    classDef delta fill:#fce4ec,stroke:#ad1457,stroke-dasharray:4 3,color:#000
+
+    Thesis["<b>Today</b>: LLMs inform humans &nbsp;&nbsp;━━ 6-month step ━━▶&nbsp;&nbsp; <b>Tomorrow</b>: LLMs act within workflows"]:::delta
+
+    subgraph P1["① Real-time bot — Mattermost"]
+        direction TB
+        U1["ePIC users"]:::human
+        B1["AI bot<br/>Haiku · cross-session memory<br/>context harness"]:::llm
+        O1["Q&A, diagnostics, on-the-fly analysis"]
+        U1 --> B1 --> O1 --> U1
+    end
+
+    subgraph P2["② Research orchestrator — corun-ai"]
+        direction TB
+        U2["Expert evaluators<br/>(production, user learning)"]:::human
+        S2["Scheduler<br/>model × sysprompt × MCP set<br/>config compare & annotate"]
+        B2["Long-latency worker<br/>Opus / Sonnet / Gemini / Gemma<br/>minutes–tens of minutes"]:::llm
+        O2["Deep research entry<br/>(e.g. Perlmutter performance)"]
+        U2 --> S2 --> B2 --> O2 --> U2
+    end
+
+    subgraph P3["③ Active workflow orchestrator — swf-testbed"]
+        direction TB
+        U3["Testbed users"]:::human
+        B3["LLM orchestrator<br/>launch · run · monitor<br/>assess · summarize"]:::llm
+        W3["Hybrid workflow<br/>LLM steps ⇄ deterministic agents<br/>DAQ sim → PanDA workers"]
+        O3["Completed run + summary"]
+        U3 --> B3 --> W3 --> B3
+        W3 --> O3 --> U3
+    end
+
+    subgraph MCP["Shared MCP tool ecosystem"]
+        direction LR
+        IH["<b>In-house</b><br/>AskPanDA · PanDA Monitor · Streaming Workflow"]:::tool
+        AD["<b>Adopted</b><br/>Rucio · XRootD · uproot · LXR · GitHub · Zenodo"]:::tool
+    end
+
+    Thesis -.-> P1
+    Thesis -.-> P2
+    Thesis -.-> P3
+    P1 --> MCP
+    P2 --> MCP
+    P3 --> MCP

docs/diagram2_mcp_ecosystem.md

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+# diagram2_mcp_ecosystem
+
+MCP ecosystem: one LLM reaches into the experiment's operational stack
+through a two-tier tool set. Answers the reviewer who thinks "everyone
+has MCP tools now" by showing depth into production systems.
+
+```mermaid
+flowchart TB
+    classDef llm fill:#e3f2fd,stroke:#1565c0,stroke-width:2px,color:#000
+    classDef ih fill:#f1f8e9,stroke:#33691e,color:#000
+    classDef ad fill:#fff8e1,stroke:#f57f17,color:#000
+    classDef sys fill:#fafafa,stroke:#888,color:#444
+
+    LLM["<b>LLM</b><br/>Opus · Sonnet · Haiku · Gemini · Gemma<br/>sysprompt · effort level · context harness"]:::llm
+
+    subgraph IH["In-house — purpose-built on our production WFMS"]
+        direction LR
+        T1["AskPanDA<br/><i>job diagnostics</i>"]:::ih
+        T2["PanDA Monitor MCP<br/><i>operational state</i>"]:::ih
+        T3["Streaming Workflow MCP<br/><i>active testbed control</i>"]:::ih
+    end
+
+    subgraph AD["3rd-party MCP — 6+ community/standard tools"]
+        direction LR
+        T4["Rucio MCP"]:::ad
+        T5["XRootD MCP"]:::ad
+        T6["uproot MCP"]:::ad
+        T7["LXR XREF MCP"]:::ad
+        T8["GitHub MCP"]:::ad
+        T9["Zenodo MCP"]:::ad
+    end
+
+    subgraph SYS["Reaches into"]
+        direction LR
+        S1["PanDA DB<br/>monitor · testbed"]:::sys
+        S2["Rucio<br/>data catalogs"]:::sys
+        S3["XRootD<br/>remote I/O"]:::sys
+        S4["ePIC codebase<br/>(55+ repos)"]:::sys
+        S5["Zenodo<br/>official repo"]:::sys
+    end
+
+    LLM --> IH
+    LLM --> AD
+    IH --> SYS
+    AD --> SYS
+```

docs/diagram3_hybrid_workflow.md

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+# diagram3_hybrid_workflow
+
+```mermaid
+flowchart TB
+    classDef llm fill:#e3f2fd,stroke:#1565c0,stroke-width:2px,color:#000
+    classDef det fill:#eeeeee,stroke:#555,color:#000
+    classDef hitl fill:#fff3e0,stroke:#e65100,stroke-dasharray:5 3,color:#000
+    classDef mcp fill:#f1f8e9,stroke:#33691e,font-size:11px,color:#000
+
+    U["User prompt<br/>'run a fast-processing test<br/>and summarize results'"]:::hitl
+
+    L1["① Prepare<br/>select config, check prior runs"]:::llm
+    L1t["swf_list_workflow_executions<br/>pcs_list_tags · swf_get_system_state"]:::mcp
+
+    L2["② Start testbed"]:::llm
+    L2t["swf_start_user_testbed"]:::mcp
+
+    L3["③ Start workflow"]:::llm
+    L3t["swf_start_workflow<br/>(stf_count, config, …)"]:::mcp
+
+    D1["④ DAQ simulator<br/>emits STF files"]:::det
+    D2["⑤ Data agent<br/>STF registration"]:::det
+    D3["⑥ FastMon agent<br/>samples Time Frames"]:::det
+    D4["⑦ Fast processing agent<br/>TF slices → PanDA"]:::det
+    D5["⑧ PanDA workers<br/>EICrecon reconstruction"]:::det
+
+    L4["⑨ Monitor in-flight<br/>errors, throughput, stragglers"]:::llm
+    L4t["swf_list_logs(level='ERROR')<br/>swf_list_workflow_executions<br/>panda_get_activity"]:::mcp
+
+    G1{"human-in-loop<br/>gate<br/>(scope of 6-mo work)"}:::hitl
+
+    L5["⑩ Assess & summarize<br/>narrative run report,<br/>anomaly notes,<br/>comparison to prior runs"]:::llm
+    L5t["swf_get_workflow_execution<br/>panda_study_job · lxr_ident"]:::mcp
+
+    O["Run entry + summary<br/>annotated, searchable"]:::hitl
+
+    U --> L1 --> L2 --> L3 --> D1 --> D2 --> D3 --> D4 --> D5 --> L4
+    L4 --> G1 --> L5 --> O
+
+    L1 -.- L1t
+    L2 -.- L2t
+    L3 -.- L3t
+    L4 -.- L4t
+    L5 -.- L5t
+```

docs/diagram3_hybrid_workflow.mmd

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+flowchart TB
+    classDef llm fill:#e3f2fd,stroke:#1565c0,stroke-width:2px,color:#000
+    classDef det fill:#eeeeee,stroke:#555,color:#000
+    classDef hitl fill:#fff3e0,stroke:#e65100,stroke-dasharray:5 3,color:#000
+    classDef mcp fill:#f1f8e9,stroke:#33691e,font-size:11px,color:#000
+
+    U["User prompt<br/>'run a fast-processing test<br/>and summarize results'"]:::hitl
+
+    L1["① Prepare<br/>select config, check prior runs"]:::llm
+    L1t["swf_list_workflow_executions<br/>pcs_list_tags · swf_get_system_state"]:::mcp
+
+    L2["② Start testbed"]:::llm
+    L2t["swf_start_user_testbed"]:::mcp
+
+    L3["③ Start workflow"]:::llm
+    L3t["swf_start_workflow<br/>(stf_count, config, …)"]:::mcp
+
+    D1["④ DAQ simulator<br/>emits STF files"]:::det
+    D2["⑤ Data agent<br/>STF registration"]:::det
+    D3["⑥ FastMon agent<br/>samples Time Frames"]:::det
+    D4["⑦ Fast processing agent<br/>TF slices → PanDA"]:::det
+    D5["⑧ PanDA workers<br/>EICrecon reconstruction"]:::det
+
+    L4["⑨ Monitor in-flight<br/>errors, throughput, stragglers"]:::llm
+    L4t["swf_list_logs(level='ERROR')<br/>swf_list_workflow_executions<br/>panda_get_activity"]:::mcp
+
+    G1{"human-in-loop<br/>gate<br/>(scope of 6-mo work)"}:::hitl
+
+    L5["⑩ Assess & summarize<br/>narrative run report,<br/>anomaly notes,<br/>comparison to prior runs"]:::llm
+    L5t["swf_get_workflow_execution<br/>panda_study_job · lxr_ident"]:::mcp
+
+    O["Run entry + summary<br/>annotated, searchable"]:::hitl
+
+    U --> L1 --> L2 --> L3 --> D1 --> D2 --> D3 --> D4 --> D5 --> L4
+    L4 --> G1 --> L5 --> O
+
+    L1 -.- L1t
+    L2 -.- L2t
+    L3 -.- L3t
+    L4 -.- L4t
+    L5 -.- L5t