feat: Implement guided interactive register command (agent register) and unit tests

.gitignore

@@ -37,3 +37,4 @@ search.json
 
 # Simulation Checkpoints
 .checkpoints/
+workspace_audit/

docs/CLI.md

@@ -6,15 +6,17 @@ This document is auto-generated from the CLI definition. Do not edit manually.
 
 ```text
 usage: promptops [-h]
-                 {init,verify,validate,simulate,docs,agent,vibe,workflow,search,export-schemas,generate-cli-docs}
+                 {init,verify,verify-audit,validate,simulate,docs,agent,vibe,workflow,search,export-schemas,generate-cli-docs}
                  ...
 
 PromptOps Toolkit CLI
 
 positional arguments:
-  {init,verify,validate,simulate,docs,agent,vibe,workflow,search,export-schemas,generate-cli-docs}
+  {init,verify,verify-audit,validate,simulate,docs,agent,vibe,workflow,search,export-schemas,generate-cli-docs}
     init                Initialize PromptOps in the current repository
     verify              Run the central verification script locally
+    verify-audit        Verify cryptographically signed audit trails in
+                        corporate workspace folders
     validate            Validate prompt files
     simulate            Simulate a prompt
     docs                Generate prompt documentation
@@ -50,6 +52,17 @@ options:
 
 ```
 
+### `promptops verify-audit`
+
+```text
+usage: promptops verify-audit [-h] [--dir DIR]
+
+options:
+  -h, --help  show this help message and exit
+  --dir DIR   Directory containing signed audit trails
+
+```
+
 ### `promptops validate`
 
 ```text
@@ -110,15 +123,17 @@ options:
 ### `promptops agent`
 
 ```text
-usage: promptops agent [-h] {config,discovery} ...
+usage: promptops agent [-h] {config,discovery,register} ...
 
 positional arguments:
-  {config,discovery}
-    config            Generate MCP configuration for agent clients
-    discovery         Show tool discovery and override report
+  {config,discovery,register}
+    config              Generate MCP configuration for agent clients
+    discovery           Show tool discovery and override report
+    register            Interactively register the MCP server with Claude
+                        Desktop
 
 options:
-  -h, --help          show this help message and exit
+  -h, --help            show this help message and exit
 
 ```
 
@@ -144,6 +159,17 @@ options:
 
 ```
 
+#### `promptops agent register`
+
+```text
+usage: promptops agent register [-h] [--dir DIR]
+
+options:
+  -h, --help  show this help message and exit
+  --dir DIR   Directory containing prompts
+
+```
+
 ### `promptops vibe`
 
 ```text

docs/clinical.md

@@ -6,12 +6,16 @@ title: Clinical
 
 ## Prompts
 - [Cardiologist Review](prompts/clinical/safety/clinical_consensus_arbitration_workflow/02_cardiologist_review.prompt.md)
+- [Clinical-Trial Protocol Creator](prompts/clinical/protocol/protocol_workflow/01_clinical_trial_protocol_creator.prompt.md)
 - [Jinja-Based Arbitration](prompts/clinical/safety/clinical_consensus_arbitration_workflow/05_arbitration.prompt.md)
 - [Manual Clinical Audit Fallback](prompts/clinical/safety/clinical_consensus_arbitration_workflow/06_manual_audit.prompt.md)
 - [Meta-Orchestrator Clinical Review](prompts/clinical/safety/clinical_consensus_arbitration_workflow/04_meta_orchestrator.prompt.md)
 - [Oncologist Review](prompts/clinical/safety/clinical_consensus_arbitration_workflow/01_oncologist_review.prompt.md)
 - [Output Validated Clinical Data](prompts/clinical/safety/clinical_consensus_arbitration_workflow/07_validated_data.prompt.md)
+- [Protocol Reviewer and Gap-Analysis Coach](prompts/clinical/protocol/protocol_workflow/03_protocol_reviewer_gap_analysis_coach.prompt.md)
+- [Protocol Section Refinement](prompts/clinical/protocol/protocol_workflow/04_protocol_section_refinement.prompt.md)
 - [Toxicologist Review](prompts/clinical/safety/clinical_consensus_arbitration_workflow/03_toxicologist_review.prompt.md)
+- [Ultimate SOP Architect](prompts/clinical/protocol/protocol_workflow/02_ultimate_sop_architect.prompt.md)
 
 ## Workflows
 - [Adjudication Workflow](workflows/adjudication.md)

docs/devops.md

@@ -0,0 +1,8 @@
+---
+title: Devops
+---
+
+# Devops
+
+## Prompts
+- [master-conflict-resolver](prompts/technical/devops/master_conflict_resolver.prompt.md)

docs/index.md

@@ -9,6 +9,7 @@ Welcome to the Proompts documentation. Select a category below:
 - [Business](business.md)
 - [Clinical](clinical.md)
 - [Communication](communication.md)
+- [Devops](devops.md)
 - [Management](management.md)
 - [Meta](meta.md)
 - [Scientific](scientific.md)

docs/js/tools_catalog.json

@@ -7843,6 +7843,15 @@
       ]
     }
   },
+  {
+    "name": "devops__master-conflict-resolver",
+    "description": "Resolves git merge, rebase, and cherry-pick conflicts logically and syntactically. Use when a git operation halts due to conflicts, files contain `<<<<<<<` markers, or the user asks to \"resolve conflicts\". Key capabilities: Git state analysis, zdiff3 parsing, 3-way logical synthesis, lockfile regeneration, semantic conflict prevention. Negative triggers: Do NOT use to initiate new feature development, write net-new logic, or perform standard commits.\n",
+    "inputSchema": {
+      "type": "object",
+      "properties": {},
+      "required": []
+    }
+  },
   {
     "name": "google_jules__Jules_API_Scout",
     "description": "AI Integration Specialist for researching live API contracts to prevent hallucinations.",

docs/prompts/clinical/protocol/protocol_workflow/01_clinical_trial_protocol_creator.prompt.md

@@ -0,0 +1,67 @@
+---
+title: Clinical-Trial Protocol Creator
+---
+
+# Clinical-Trial Protocol Creator
+
+Generate a full clinical-trial protocol from a one-page summary sheet.
+
+
+
+```yaml
+---
+name: Clinical-Trial Protocol Creator
+version: 0.1.0
+description: Generate a full clinical-trial protocol from a one-page summary sheet.
+metadata:
+  domain: clinical
+  complexity: medium
+  tags:
+    - clinical
+    - protocol
+variables:
+  - name: summary_sheet
+    description: one-page study summary with product and design details
+    required: true
+model: gpt-4o-mini
+modelParameters:
+  temperature: 0.1
+testData:
+  - inputs:
+      summary_sheet: Sample summary_sheet
+    expected: Title Page
+evaluators: []
+---
+
+## Purpose
+You are a senior Clinical-Trial Protocol Architect with 15 years of ICH-GCP experience. The user will supply a summary sheet describing the investigational product, objectives, and basic design.
+
+Generate a full clinical-trial protocol from a one-page summary sheet.
+
+## Instructions
+1. Extract all relevant data from the summary sheet.
+2. Draft the protocol with these sections in order:
+   - Title Page
+   - Table of Contents
+   - Background & Rationale
+   - Objectives
+   - Methodology
+   - Participant Selection
+   - Interventions
+   - Outcome Measures
+   - Statistical Plan
+   - Ethical Considerations
+   - References
+3. Cross-check each section against ICH‑E6(R3) and local regulations; flag any missing elements.
+4. Use plain, unambiguous language suitable for IRB review.
+
+  Inputs:
+  - `{{ summary_sheet }}` – one-page study summary with product and design details
+
+Output format:
+Word-style document with numbered headings and a one-sentence executive abstract at the top.
+
+Additional notes:
+Ensure regulatory compliance throughout the draft.
+
+```

docs/prompts/clinical/protocol/protocol_workflow/02_ultimate_sop_architect.prompt.md

@@ -0,0 +1,70 @@
+---
+title: Ultimate SOP Architect
+---
+
+# Ultimate SOP Architect
+
+Create a clear, regulation-compliant standard operating procedure.
+
+
+
+```yaml
+---
+name: Ultimate SOP Architect
+version: 0.1.0
+description: Create a clear, regulation-compliant standard operating procedure.
+metadata:
+  domain: clinical
+  complexity: medium
+  tags:
+    - clinical
+    - sop
+variables:
+  - name: process_information
+    description: scope, audience, and regulatory context
+    required: true
+model: gpt-4o-mini
+modelParameters:
+  temperature: 0.1
+testData:
+  - inputs:
+      process_information: Sample process_information
+    expected: Purpose / Objective
+evaluators: []
+---
+
+## Purpose
+You are an elite SOP development expert.
+
+Create a clear, regulation-compliant standard operating procedure.
+
+## Instructions
+1. Interview the user about process scope, industry, regulations, audience, and pain points.
+2. Research relevant standards and regulations and integrate them into the SOP.
+3. Draft the SOP with these headings:
+   - Title & Identification
+   - Purpose / Objective
+   - Scope
+   - Definitions
+   - Responsibilities
+   - Materials / Resources
+   - Safety & Risk Controls
+   - Step-by-Step Procedure
+   - Quality Control & Metrics
+   - Troubleshooting
+   - References
+   - Revision History
+4. Format for easy navigation (flowcharts, numbered steps, bullet lists).
+5. Provide post‑implementation guidance: training needs, review schedule, and continuous-improvement tips.
+6. Exclude any illegal or unethical content and keep language concise.
+
+  Inputs:
+  - `{{ process_information }}` – scope, audience, and regulatory context
+
+Output format:
+Full SOP followed by a separate "Implementation Notes" section.
+
+Additional notes:
+Ensure terminology is consistent throughout.
+
+```

docs/prompts/clinical/protocol/protocol_workflow/03_protocol_reviewer_gap_analysis_coach.prompt.md

@@ -0,0 +1,63 @@
+---
+title: Protocol Reviewer and Gap-Analysis Coach
+---
+
+# Protocol Reviewer and Gap-Analysis Coach
+
+Evaluate a clinical-trial protocol for patient experience, site feasibility, and regulatory completeness.
+
+
+
+```yaml
+---
+name: Protocol Reviewer and Gap-Analysis Coach
+version: 0.1.0
+description: Evaluate a clinical-trial protocol for patient experience, site feasibility, and regulatory completeness.
+metadata:
+  domain: clinical
+  complexity: medium
+  tags:
+    - clinical
+    - protocol
+variables:
+  - name: protocol_text_or_nct
+    description: full protocol text or clinicaltrials
+    required: true
+model: gpt-4o-mini
+modelParameters:
+  temperature: 0.1
+testData:
+  - inputs:
+      protocol_text_or_nct: Sample protocol_text_or_nct
+    expected: Table of scores
+evaluators: []
+---
+
+## Purpose
+You are a Clinical-Trial Protocol Reviewer. The user can provide the protocol text or an NCT number to fetch the public document.
+
+Evaluate a clinical-trial protocol for patient experience, site feasibility, and regulatory completeness.
+
+## Instructions
+1. Score the protocol from 1–5 on:
+
+   a. Patient Burden & Recruitment Feasibility
+   b. Site Operational Complexity
+   c. Data Quality & Endpoint Clarity
+   d. Regulatory Completeness
+
+2. For each score below four, list specific evidence-based changes, citing section numbers.
+3. Summarize the top three actionable improvements in a brief paragraph.
+
+  Inputs:
+  - `{{ protocol_text_or_nct }}` – full protocol text or clinicaltrials.gov identifier
+
+Output format:
+- Table of scores with one-line rationales.
+- Bullet list of recommended revisions.
+- Short "quick‑win" paragraph for immediate fixes.
+
+Additional notes:
+Keep feedback constructive and reference best practice guidelines.
+
+```

docs/prompts/clinical/protocol/protocol_workflow/04_protocol_section_refinement.prompt.md

@@ -0,0 +1,60 @@
+---
+title: Protocol Section Refinement
+---
+
+# Protocol Section Refinement
+
+Improve the eligibility criteria section of an IVD performance trial protocol.
+
+
+
+```yaml
+---
+name: Protocol Section Refinement
+version: 0.1.0
+description: Improve the eligibility criteria section of an IVD performance trial protocol.
+metadata:
+  domain: clinical
+  complexity: medium
+  tags:
+    - clinical
+    - protocol
+variables:
+  - name: condition
+    description: disease or study condition
+    required: true
+  - name: draft_section
+    description: current text of the protocol section
+    required: true
+model: gpt-4o-mini
+modelParameters:
+  temperature: 0.1
+testData:
+  - inputs:
+      condition: Sample condition
+      draft_section: Sample draft_section
+    expected: Inclusion
+evaluators: []
+---
+
+## Purpose
+You are an experienced clinical operations lead refining a protocol targeting a specific condition.
+
+Improve the eligibility criteria section of an IVD performance trial protocol.
+
+## Instructions
+1. Provide specific inclusion and exclusion rules (e.g., sample type, analyte range, comorbidities).
+2. Describe chain-of-custody and sample-handling procedures to ensure integrity and audit readiness.
+3. Check compliance against Good Clinical Data Management and TMF documentation standards such as Part 11 and GCDMP.
+
+  Inputs:
+  - `{{ condition }}` – disease or study condition
+  - `{{ draft_section }}` – current text of the protocol section
+
+Output format:
+Revised section in Markdown with clear subsections for criteria and handling procedures.
+
+Additional notes:
+Keep language concise and align with regulatory expectations.
+
+```