Change the commands from vibepaper to copaper and add github pages

.agents/skills/AGENTS.md

@@ -2,10 +2,10 @@
 
 ## OVERVIEW
 ###### Skill catalog for writing and workflow automation
-<!-- description: Purpose of the skills directory and its role in VibePaper -->
-The `.agents/skills/` directory contains the reusable skill library shipped with VibePaper.
+<!-- description: Purpose of the skills directory and its role in CoPaper -->
+The `.agents/skills/` directory contains the reusable skill library shipped with CoPaper.
 Each skill is a self-contained module that extends the agent's capabilities for a specific academic task or workflow-management task.
-These skills are bundled into initialized projects by `vibe init`.
+These skills are bundled into initialized projects by `copaper init`.
 
 ## STRUCTURE
 ###### Standardized skill module organization
@@ -18,9 +18,9 @@ These skills are bundled into initialized projects by `vibe init`.
 ## WHERE TO LOOK
 ###### Important skills in the current catalog
 <!-- description: Catalog of skills in this directory -->
-- `vibepaper-manage`: Teaches agents how to use OpenCode plugin tools for dashboard, initialization, artifact readiness, workflow status, phase updates, and workflow log inspection.
+- `copaper-manage`: Teaches agents how to use OpenCode plugin tools for dashboard, initialization, artifact readiness, workflow status, phase updates, and workflow log inspection.
 - `human-comment-helper`: Adds structured reviewer feedback and synthetic examples.
-- `latex2markdown`: Imports content from LaTeX files into the VibePaper structure.
+- `latex2markdown`: Imports content from LaTeX files into the CoPaper structure.
 - `markdown-helper`: Interactive assistance for writing and improving `paper.md`.
 - `markdown-review`: Quality assurance check for novelty, importance, and correctness.
 - `markdown2latex`: High-quality export from `paper.md` to conference-ready LaTeX.
@@ -40,19 +40,19 @@ These skills are bundled into initialized projects by `vibe init`.
 - **Quality Gates**: Use `markdown-review` to validate content before final export.
 - **Format Mapping**: Conversion skills must maintain semantic meaning across formats.
 - **Math Support**: Preserve `$...$` and `$$...$$` during all transformations.
-- **OpenCode Plugin Tools**: When available, skills MUST use `vibepaper_dashboard`, `vibepaper_init_apply`, `vibepaper_artifact_status`, `vibepaper_artifact_record`, `vibepaper_workflow_status`, `vibepaper_workflow_log`, and `vibepaper_workflow_set_phase` instead of shell `vibe` commands or manual `.agents/state.json` / `.agents/events.jsonl` edits.
-- **Project Initialization**: After explicit user confirmation and collection of project `name` and `domain`, call `vibepaper_init_apply` to initialize OpenCode-managed VibePaper core files. Do not describe initialization as a prompt-only action or manually create the core files when the plugin tool is available.
-- **Workflow Status Queries**: For read-only workflow phase status, current phase, phase table, and next-step recommendation, call `vibepaper_workflow_status`. Do not read `.agents/state.json` directly for phase state when the plugin tool is available.
-- **Paper Structure Queries**: For read-only `paper.md` Level 2-5 completion, Level 5 writing targets, next writing target, and structural issues, call `vibepaper_paper_structure_status`. Do not reimplement this as prompt-only heading scans or shell parsing when the plugin tool is available.
-- **Storyline Structure Queries**: For read-only `storyline.md` `#####` section readiness, TODO coverage, and next storyline target, call `vibepaper_storyline_structure_status`. Do not reimplement this as prompt-only section scans when the plugin tool is available.
-- **Import Extraction**: For user-specified PDF and PPTX imports, call `vibepaper_pdf_extract` or `vibepaper_ppt_extract`. These tools are read-only and require an explicit user-provided absolute or relative path; do not run separate shell existence checks, scan directories, glob for candidates, or guess source files.
-- **Checker Status Queries**: For read-only checker run status, Critical/Major/Minor counts, stale signals, and `.agents/precheck_report.md` evidence, call `vibepaper_checker_status`. Do not read `.agents/state.json` or `.agents/precheck_report.md` directly just to infer checker status when the plugin tool is available.
-- **Reviewer Boundary**: Route checker review, checker-result summarization, and issue explanation to `@vibepaper-reviewer` when available. The reviewer is read-only and must not edit `paper.md` or write checker records directly.
-- **Phase Updates**: After explicit user confirmation, call `vibepaper_workflow_set_phase`; the tool writes `.agents/state.json` and appends `.agents/events.jsonl`. Do not describe this as a prompt-only action.
-- **Workflow Log Queries**: For read-only inspection of `.agents/events.jsonl`, call `vibepaper_workflow_log` with optional `lastN`, `phase`, and `operator` filters. Do not read the event log file directly when the plugin tool is available.
-- **Artifact Readiness Queries**: For read-only artifact readiness, evidence, confidence, and recommendation, call `vibepaper_artifact_status`. Do not manually infer readiness from files or `.agents/state.json` when the plugin tool is available.
-- **Artifact Readiness Records**: After explicit user confirmation, route artifact readiness recording to `@vibepaper-recorder`; the recorder calls `vibepaper_artifact_record`, which writes the `artifacts` area in `.agents/state.json` and appends `.agents/events.jsonl`. Do not describe readiness recording as a prompt-only action.
-- **Recorder Boundary**: `vibepaper_artifact_record` must be invoked through `@vibepaper-recorder`; other agents should route the recording action rather than calling it directly.
+- **OpenCode Plugin Tools**: When available, skills MUST use `copaper_dashboard`, `copaper_init_apply`, `copaper_artifact_status`, `copaper_artifact_record`, `copaper_workflow_status`, `copaper_workflow_log`, and `copaper_workflow_set_phase` instead of shell `copaper` commands or manual `.agents/state.json` / `.agents/events.jsonl` edits.
+- **Project Initialization**: After explicit user confirmation and collection of project `name` and `domain`, call `copaper_init_apply` to initialize OpenCode-managed CoPaper core files. Do not describe initialization as a prompt-only action or manually create the core files when the plugin tool is available.
+- **Workflow Status Queries**: For read-only workflow phase status, current phase, phase table, and next-step recommendation, call `copaper_workflow_status`. Do not read `.agents/state.json` directly for phase state when the plugin tool is available.
+- **Paper Structure Queries**: For read-only `paper.md` Level 2-5 completion, Level 5 writing targets, next writing target, and structural issues, call `copaper_paper_structure_status`. Do not reimplement this as prompt-only heading scans or shell parsing when the plugin tool is available.
+- **Storyline Structure Queries**: For read-only `storyline.md` `#####` section readiness, TODO coverage, and next storyline target, call `copaper_storyline_structure_status`. Do not reimplement this as prompt-only section scans when the plugin tool is available.
+- **Import Extraction**: For user-specified PDF and PPTX imports, call `copaper_pdf_extract` or `copaper_ppt_extract`. These tools are read-only and require an explicit user-provided absolute or relative path; do not run separate shell existence checks, scan directories, glob for candidates, or guess source files.
+- **Checker Status Queries**: For read-only checker run status, Critical/Major/Minor counts, stale signals, and `.agents/precheck_report.md` evidence, call `copaper_checker_status`. Do not read `.agents/state.json` or `.agents/precheck_report.md` directly just to infer checker status when the plugin tool is available.
+- **Reviewer Boundary**: Route checker review, checker-result summarization, and issue explanation to `@copaper-reviewer` when available. The reviewer is read-only and must not edit `paper.md` or write checker records directly.
+- **Phase Updates**: After explicit user confirmation, call `copaper_workflow_set_phase`; the tool writes `.agents/state.json` and appends `.agents/events.jsonl`. Do not describe this as a prompt-only action.
+- **Workflow Log Queries**: For read-only inspection of `.agents/events.jsonl`, call `copaper_workflow_log` with optional `lastN`, `phase`, and `operator` filters. Do not read the event log file directly when the plugin tool is available.
+- **Artifact Readiness Queries**: For read-only artifact readiness, evidence, confidence, and recommendation, call `copaper_artifact_status`. Do not manually infer readiness from files or `.agents/state.json` when the plugin tool is available.
+- **Artifact Readiness Records**: After explicit user confirmation, route artifact readiness recording to `@copaper-recorder`; the recorder calls `copaper_artifact_record`, which writes the `artifacts` area in `.agents/state.json` and appends `.agents/events.jsonl`. Do not describe readiness recording as a prompt-only action.
+- **Recorder Boundary**: `copaper_artifact_record` must be invoked through `@copaper-recorder`; other agents should route the recording action rather than calling it directly.
 - **Unsupported Tool Gaps**: If the OpenCode plugin does not yet expose a needed capability, state the gap explicitly instead of inventing a plugin tool or falling back silently.
 - **Scaffold Sync**: New or changed skills must be mirrored into the packaged scaffold.
 

.agents/skills/auto-init/SKILL.md

@@ -1,11 +1,11 @@
 ---
 name: auto-init
-description: Detect when the user wants to start a new VibePaper paper project or initialize a workspace, run `vibe --root . init` when needed, then inspect the current workflow phase and immediately begin the appropriate next phase work.
+description: Detect when the user wants to start a new CoPaper paper project or initialize a workspace, run `copaper --root . init` when needed, then inspect the current workflow phase and immediately begin the appropriate next phase work.
 ---
 
 # Auto Init
 
-This skill initializes a VibePaper project when the user expresses intent to start a new paper or workspace.
+This skill initializes a CoPaper project when the user expresses intent to start a new paper or workspace.
 
 ## Input Files
 
@@ -18,7 +18,7 @@ This skill initializes a VibePaper project when the user expresses intent to sta
 
 ## Triggers
 
-Use this skill when the user asks to start or initialize a VibePaper paper project, including phrases such as:
+Use this skill when the user asks to start or initialize a CoPaper paper project, including phrases such as:
 
 - "start working"
 - "start writing paper"
@@ -38,7 +38,7 @@ Use this skill when the user asks to start or initialize a VibePaper paper proje
 5. Run:
 
 ```bash
-vibe --root . init --name "<project_name>" --domain "<domain>"
+copaper --root . init --name "<project_name>" --domain "<domain>"
 ```
 
 6. After initialization succeeds, tell the user where the scaffold was created.
@@ -54,14 +54,14 @@ Only run `git init` when `command -v git` succeeds and `git rev-parse --is-insid
 8. Continue immediately by checking status:
 
 ```bash
-vibe --root . status --json
+copaper --root . status --json
 ```
 
 9. Read `current_phase` from the JSON output and begin that phase's work without waiting for another user command.
 
 ## Phase Continuation
 
-After `vibe --root . status --json`, use this routing:
+After `copaper --root . status --json`, use this routing:
 
 | Current Phase | Begin This Work |
 |---------------|-----------------|
@@ -80,5 +80,5 @@ If the phase requires information the user has not provided, ask only for the mi
 - Keep `--root` before the `init` subcommand.
 - Use the CLI for initialization instead of manually creating `.agents/state.json`.
 - Do not run `git init` when the current folder is already inside an existing Git work tree.
-- Do not require Git; if it is unavailable, continue the VibePaper workflow.
+- Do not require Git; if it is unavailable, continue the CoPaper workflow.
 - Do not stop after initialization when status can be read; continue into the current phase workflow.

.agents/skills/bogus-data-helper/SKILL.md

@@ -28,7 +28,7 @@ You are an AI assistant helping create placeholder evaluation data. Your generat
 
 ## Paper Structure Reference
 
-The paper follows VibePaper structure. Key rules for inserting placeholder content:
+The paper follows CoPaper structure. Key rules for inserting placeholder content:
 - **Level 1** (`#`): Paper title only.
 - **Level 2-5** (`##` to `#####`): Structural headings only — do NOT modify these.
 - **Level 6** (`######`): Content paragraphs. Title = topic sentence (≤50 chars). Body = supporting text (≤500 chars).

.agents/skills/clarity-checker/SKILL.md

@@ -5,7 +5,7 @@ description: Detects undefined terms, unclear descriptions, and clarity issues i
 
 # Clarity Checker Skill
 
-This skill identifies clarity issues in academic paper drafts following the VibePaper structure, including undefined terms, vague descriptions, ambiguous references, and insufficient explanations that hinder reader comprehension.
+This skill identifies clarity issues in academic paper drafts following the CoPaper structure, including undefined terms, vague descriptions, ambiguous references, and insufficient explanations that hinder reader comprehension.
 
 ## When to Use This Skill
 
@@ -239,7 +239,7 @@ For each clarity issue found:
 
 ## Paper Structure Reference
 
-The paper follows VibePaper structure. Key rules for this checker:
+The paper follows CoPaper structure. Key rules for this checker:
 - **Level 1-5** (`#` to `#####`): Structural headings only — no body text allowed under these.
 - **Level 6** (`######`): Content paragraphs. Title = topic sentence (≤50 chars). Body = supporting text (≤500 chars).
 - **Metadata**: HTML comments `<!-- description: ... -->` guide what each section should contain.