research-copilot 0.1.0

package/app/out/renderer/assets/yacas-b5lAVEIl.js

@@ -0,0 +1,130 @@
+function words(str) {
+  var obj = {}, words2 = str.split(" ");
+  for (var i = 0; i < words2.length; ++i) obj[words2[i]] = true;
+  return obj;
+}
+var bodiedOps = words("Assert BackQuote D Defun Deriv For ForEach FromFile FromString Function Integrate InverseTaylor Limit LocalSymbols Macro MacroRule MacroRulePattern NIntegrate Rule RulePattern Subst TD TExplicitSum TSum Taylor Taylor1 Taylor2 Taylor3 ToFile ToStdout ToString TraceRule Until While");
+var pFloatForm = "(?:(?:\\.\\d+|\\d+\\.\\d*|\\d+)(?:[eE][+-]?\\d+)?)";
+var pIdentifier = "(?:[a-zA-Z\\$'][a-zA-Z0-9\\$']*)";
+var reFloatForm = new RegExp(pFloatForm);
+var reIdentifier = new RegExp(pIdentifier);
+var rePattern = new RegExp(pIdentifier + "?_" + pIdentifier);
+var reFunctionLike = new RegExp(pIdentifier + "\\s*\\(");
+function tokenBase(stream, state) {
+  var ch;
+  ch = stream.next();
+  if (ch === '"') {
+    state.tokenize = tokenString;
+    return state.tokenize(stream, state);
+  }
+  if (ch === "/") {
+    if (stream.eat("*")) {
+      state.tokenize = tokenComment;
+      return state.tokenize(stream, state);
+    }
+    if (stream.eat("/")) {
+      stream.skipToEnd();
+      return "comment";
+    }
+  }
+  stream.backUp(1);
+  var m = stream.match(/^(\w+)\s*\(/, false);
+  if (m !== null && bodiedOps.hasOwnProperty(m[1]))
+    state.scopes.push("bodied");
+  var scope = currentScope(state);
+  if (scope === "bodied" && ch === "[")
+    state.scopes.pop();
+  if (ch === "[" || ch === "{" || ch === "(")
+    state.scopes.push(ch);
+  scope = currentScope(state);
+  if (scope === "[" && ch === "]" || scope === "{" && ch === "}" || scope === "(" && ch === ")")
+    state.scopes.pop();
+  if (ch === ";") {
+    while (scope === "bodied") {
+      state.scopes.pop();
+      scope = currentScope(state);
+    }
+  }
+  if (stream.match(/\d+ *#/, true, false)) {
+    return "qualifier";
+  }
+  if (stream.match(reFloatForm, true, false)) {
+    return "number";
+  }
+  if (stream.match(rePattern, true, false)) {
+    return "variableName.special";
+  }
+  if (stream.match(/(?:\[|\]|{|}|\(|\))/, true, false)) {
+    return "bracket";
+  }
+  if (stream.match(reFunctionLike, true, false)) {
+    stream.backUp(1);
+    return "variableName.function";
+  }
+  if (stream.match(reIdentifier, true, false)) {
+    return "variable";
+  }
+  if (stream.match(/(?:\\|\+|\-|\*|\/|,|;|\.|:|@|~|=|>|<|&|\||_|`|'|\^|\?|!|%|#)/, true, false)) {
+    return "operator";
+  }
+  return "error";
+}
+function tokenString(stream, state) {
+  var next, end = false, escaped = false;
+  while ((next = stream.next()) != null) {
+    if (next === '"' && !escaped) {
+      end = true;
+      break;
+    }
+    escaped = !escaped && next === "\\";
+  }
+  if (end && !escaped) {
+    state.tokenize = tokenBase;
+  }
+  return "string";
+}
+function tokenComment(stream, state) {
+  var prev, next;
+  while ((next = stream.next()) != null) {
+    if (prev === "*" && next === "/") {
+      state.tokenize = tokenBase;
+      break;
+    }
+    prev = next;
+  }
+  return "comment";
+}
+function currentScope(state) {
+  var scope = null;
+  if (state.scopes.length > 0)
+    scope = state.scopes[state.scopes.length - 1];
+  return scope;
+}
+const yacas = {
+  name: "yacas",
+  startState: function() {
+    return {
+      tokenize: tokenBase,
+      scopes: []
+    };
+  },
+  token: function(stream, state) {
+    if (stream.eatSpace()) return null;
+    return state.tokenize(stream, state);
+  },
+  indent: function(state, textAfter, cx) {
+    if (state.tokenize !== tokenBase && state.tokenize !== null)
+      return null;
+    var delta = 0;
+    if (textAfter === "]" || textAfter === "];" || textAfter === "}" || textAfter === "};" || textAfter === ");")
+      delta = -1;
+    return (state.scopes.length + delta) * cx.unit;
+  },
+  languageData: {
+    electricInput: /[{}\[\]()\;]/,
+    commentTokens: { line: "//", block: { open: "/*", close: "*/" } }
+  }
+};
+export {
+  yacas
+};

package/app/out/renderer/assets/z80-BZV19vqv.js

@@ -0,0 +1,93 @@
+function mkZ80(ez802) {
+  var keywords1, keywords2;
+  if (ez802) {
+    keywords1 = /^(exx?|(ld|cp)([di]r?)?|[lp]ea|pop|push|ad[cd]|cpl|daa|dec|inc|neg|sbc|sub|and|bit|[cs]cf|x?or|res|set|r[lr]c?a?|r[lr]d|s[lr]a|srl|djnz|nop|[de]i|halt|im|in([di]mr?|ir?|irx|2r?)|ot(dmr?|[id]rx|imr?)|out(0?|[di]r?|[di]2r?)|tst(io)?|slp)(\.([sl]?i)?[sl])?\b/i;
+    keywords2 = /^(((call|j[pr]|rst|ret[in]?)(\.([sl]?i)?[sl])?)|(rs|st)mix)\b/i;
+  } else {
+    keywords1 = /^(exx?|(ld|cp|in)([di]r?)?|pop|push|ad[cd]|cpl|daa|dec|inc|neg|sbc|sub|and|bit|[cs]cf|x?or|res|set|r[lr]c?a?|r[lr]d|s[lr]a|srl|djnz|nop|rst|[de]i|halt|im|ot[di]r|out[di]?)\b/i;
+    keywords2 = /^(call|j[pr]|ret[in]?|b_?(call|jump))\b/i;
+  }
+  var variables1 = /^(af?|bc?|c|de?|e|hl?|l|i[xy]?|r|sp)\b/i;
+  var variables2 = /^(n?[zc]|p[oe]?|m)\b/i;
+  var errors = /^([hl][xy]|i[xy][hl]|slia|sll)\b/i;
+  var numbers = /^([\da-f]+h|[0-7]+o|[01]+b|\d+d?)\b/i;
+  return {
+    name: "z80",
+    startState: function() {
+      return {
+        context: 0
+      };
+    },
+    token: function(stream, state) {
+      if (!stream.column())
+        state.context = 0;
+      if (stream.eatSpace())
+        return null;
+      var w;
+      if (stream.eatWhile(/\w/)) {
+        if (ez802 && stream.eat(".")) {
+          stream.eatWhile(/\w/);
+        }
+        w = stream.current();
+        if (stream.indentation()) {
+          if ((state.context == 1 || state.context == 4) && variables1.test(w)) {
+            state.context = 4;
+            return "variable";
+          }
+          if (state.context == 2 && variables2.test(w)) {
+            state.context = 4;
+            return "variableName.special";
+          }
+          if (keywords1.test(w)) {
+            state.context = 1;
+            return "keyword";
+          } else if (keywords2.test(w)) {
+            state.context = 2;
+            return "keyword";
+          } else if (state.context == 4 && numbers.test(w)) {
+            return "number";
+          }
+          if (errors.test(w))
+            return "error";
+        } else if (stream.match(numbers)) {
+          return "number";
+        } else {
+          return null;
+        }
+      } else if (stream.eat(";")) {
+        stream.skipToEnd();
+        return "comment";
+      } else if (stream.eat('"')) {
+        while (w = stream.next()) {
+          if (w == '"')
+            break;
+          if (w == "\\")
+            stream.next();
+        }
+        return "string";
+      } else if (stream.eat("'")) {
+        if (stream.match(/\\?.'/))
+          return "number";
+      } else if (stream.eat(".") || stream.sol() && stream.eat("#")) {
+        state.context = 5;
+        if (stream.eatWhile(/\w/))
+          return "def";
+      } else if (stream.eat("$")) {
+        if (stream.eatWhile(/[\da-f]/i))
+          return "number";
+      } else if (stream.eat("%")) {
+        if (stream.eatWhile(/[01]/))
+          return "number";
+      } else {
+        stream.next();
+      }
+      return null;
+    }
+  };
+}
+const z80 = mkZ80(false);
+const ez80 = mkZ80(true);
+export {
+  ez80,
+  z80
+};

package/app/out/renderer/index.html

@@ -0,0 +1,13 @@
+<!doctype html>
+<html lang="en" class="dark">
+  <head>
+    <meta charset="UTF-8" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+    <title>Research Pilot</title>
+    <script type="module" crossorigin src="./assets/index-BqDyyRCx.js"></script>
+    <link rel="stylesheet" crossorigin href="./assets/index-C-_uCjZJ.css">
+  </head>
+  <body class="overflow-hidden">
+    <div id="root"></div>
+  </body>
+</html>

package/app/out/skills/community-builtin/README.md

@@ -0,0 +1,29 @@
+# Community Built-in Skills
+
+This directory contains framework-integrated community skills using open directory format:
+
+```text
+src/skills/community-builtin/<skill-id>/SKILL.md
+src/skills/community-builtin/<skill-id>/scripts/*
+```
+
+Project-local user skills use the same layout under:
+
+```text
+.agentfoundry/skills/<skill-id>/SKILL.md
+.agentfoundry/skills/<skill-id>/scripts/*
+```
+
+Included examples:
+- `repo-quick-audit`
+- `markitdown`
+- `document-docx`
+
+Research Pilot-specific default project skills live in:
+
+```text
+examples/research-pilot/skills/default-project-skills
+```
+
+Build note:
+- `npm run build` copies this directory to `dist/skills/community-builtin` so published packages can load community skills without source files.

package/app/out/skills/community-builtin/document-docx/SKILL.md

@@ -0,0 +1,44 @@
+---
+name: document-skills-docx
+description: Read, convert, and structure DOCX documents for drafting workflows.
+allowed-tools:
+  - skill-script-run
+id: document-docx
+shortDescription: DOCX extraction and conversion workflow for manuscript drafting
+loadingStrategy: lazy
+tools:
+  - skill-script-run
+tags:
+  - community
+  - docx
+  - document-processing
+meta:
+  approvedByUser: true
+  capabilities:
+    convert_to_markdown:
+      script: docx-to-markdown
+      extensions:
+        - docx
+  upstream:
+    repo: https://github.com/K-Dense-AI/claude-scientific-writer
+    path: skills/document-skills/docx
+---
+
+# Summary
+Use this skill for DOCX-first workflows: extract text, convert to markdown, and scaffold structured drafts.
+
+## Procedures
+1. Prepare DOCX tooling once in the environment.
+2. Convert `.docx` to markdown for tool-friendly editing.
+3. Extract raw text when markdown conversion fails or formatting is noisy.
+4. Create a clean DOCX template for collaborative writing handoff.
+
+## Scripts
+- `setup-docx-tools`: Install conversion dependencies.
+- `docx-to-markdown`: Convert DOCX to Markdown.
+- `extract-docx-text`: Dump plain text from DOCX.
+- `init-docx-template`: Generate a minimal DOCX template file.
+
+## Notes
+- Prefer markdown as intermediate editing format.
+- Keep the original DOCX unchanged; write outputs to new files.

package/app/out/skills/community-builtin/document-docx/scripts/docx-to-markdown.sh

@@ -0,0 +1,20 @@
+#!/usr/bin/env bash
+set -euo pipefail
+
+if [ "$#" -lt 2 ]; then
+  echo "Usage: docx-to-markdown.sh <input.docx> <output.md>" >&2
+  exit 1
+fi
+
+INPUT_PATH="$1"
+OUTPUT_PATH="$2"
+
+if command -v markitdown >/dev/null 2>&1; then
+  markitdown "$INPUT_PATH" -o "$OUTPUT_PATH"
+elif command -v pandoc >/dev/null 2>&1; then
+  pandoc "$INPUT_PATH" -f docx -t markdown -o "$OUTPUT_PATH"
+else
+  uvx --from "markitdown[all]" markitdown "$INPUT_PATH" -o "$OUTPUT_PATH"
+fi
+
+echo "converted: $INPUT_PATH -> $OUTPUT_PATH"

package/app/out/skills/community-builtin/document-docx/scripts/extract-docx-text.sh

@@ -0,0 +1,28 @@
+#!/usr/bin/env bash
+set -euo pipefail
+
+if [ "$#" -lt 2 ]; then
+  echo "Usage: extract-docx-text.sh <input.docx> <output.txt>" >&2
+  exit 1
+fi
+
+INPUT_PATH="$1"
+OUTPUT_PATH="$2"
+
+if ! python3 -c "from docx import Document" >/dev/null 2>&1; then
+  echo "python-docx is not installed. Run setup-docx-tools.sh first." >&2
+  exit 1
+fi
+
+python3 - "$INPUT_PATH" "$OUTPUT_PATH" <<'PY'
+import sys
+from docx import Document
+
+src, dst = sys.argv[1], sys.argv[2]
+doc = Document(src)
+lines = [p.text for p in doc.paragraphs]
+with open(dst, "w", encoding="utf-8") as f:
+    f.write("\n".join(lines))
+PY
+
+echo "extracted text: $INPUT_PATH -> $OUTPUT_PATH"

package/app/out/skills/community-builtin/document-docx/scripts/init-docx-template.sh

@@ -0,0 +1,32 @@
+#!/usr/bin/env bash
+set -euo pipefail
+
+if [ "$#" -lt 1 ]; then
+  echo "Usage: init-docx-template.sh <output.docx>" >&2
+  exit 1
+fi
+
+OUTPUT_PATH="$1"
+
+if ! python3 -c "from docx import Document" >/dev/null 2>&1; then
+  echo "python-docx is not installed. Run setup-docx-tools.sh first." >&2
+  exit 1
+fi
+
+python3 - "$OUTPUT_PATH" <<'PY'
+import sys
+from docx import Document
+
+dst = sys.argv[1]
+doc = Document()
+doc.add_heading("Document Title", level=1)
+doc.add_paragraph("Author: ")
+doc.add_paragraph("Date: ")
+doc.add_heading("Abstract", level=2)
+doc.add_paragraph("")
+doc.add_heading("Main Content", level=2)
+doc.add_paragraph("")
+doc.save(dst)
+PY
+
+echo "template created: $OUTPUT_PATH"

package/app/out/skills/community-builtin/document-docx/scripts/setup-docx-tools.sh

@@ -0,0 +1,10 @@
+#!/usr/bin/env bash
+set -euo pipefail
+
+if command -v uv >/dev/null 2>&1; then
+  uv pip install "markitdown[all]" "python-docx>=1.1.0"
+else
+  python3 -m pip install --user "markitdown[all]" "python-docx>=1.1.0"
+fi
+
+echo "docx tools setup complete"

package/app/out/skills/community-builtin/markitdown/SKILL.md

@@ -0,0 +1,105 @@
+---
+name: markitdown
+description: Convert files and office documents to Markdown. Supports PDF, DOCX, PPTX, XLSX, images (with OCR), audio (with transcription), HTML, CSV, JSON, XML, ZIP, YouTube URLs, EPubs and more.
+allowed-tools:
+  - skill-script-run
+license: MIT
+source: https://github.com/microsoft/markitdown
+id: markitdown
+shortDescription: Convert local files to Markdown via Microsoft MarkItDown
+loadingStrategy: lazy
+tools:
+  - skill-script-run
+tags:
+  - community
+  - document-conversion
+  - markdown
+meta:
+  approvedByUser: true
+  capabilities:
+    convert_to_markdown:
+      script: convert-file
+      extensions:
+        - pdf
+        - docx
+        - pptx
+        - xlsx
+        - csv
+        - html
+        - json
+        - xml
+        - txt
+        - md
+        - epub
+  upstream:
+    repo: https://github.com/K-Dense-AI/claude-scientific-writer
+    path: skills/markitdown
+---
+
+# MarkItDown - File to Markdown Conversion
+
+## Overview
+
+MarkItDown converts many document and media formats into Markdown optimized for LLM workflows.
+
+Use this skill when you need to:
+- Convert research papers and reports into markdown for analysis
+- Extract text from office files or scanned docs
+- Normalize heterogeneous source files before indexing/RAG
+
+## Preferred Workflow in AgentFoundry
+
+1. Ensure tool availability:
+- Use `skill-script-run` and run script `setup-markitdown` once per environment.
+
+2. Convert a single file:
+- Run script `convert-file` with input path and output path.
+
+3. Batch convert:
+- Run script `batch-convert` with input directory and output directory.
+
+4. Validate quality:
+- Read output markdown and check tables, equations, and OCR-heavy sections.
+
+## Script Interface
+
+### `setup-markitdown`
+
+Install MarkItDown with broad format support:
+
+```bash
+skill-script-run {
+  "skillId": "markitdown",
+  "script": "setup-markitdown"
+}
+```
+
+### `convert-file`
+
+Convert one file to markdown:
+
+```bash
+skill-script-run {
+  "skillId": "markitdown",
+  "script": "convert-file",
+  "args": ["input.pdf", "output.md"]
+}
+```
+
+### `batch-convert`
+
+Convert all supported files in a directory:
+
+```bash
+skill-script-run {
+  "skillId": "markitdown",
+  "script": "batch-convert",
+  "args": ["./docs", "./markdown"]
+}
+```
+
+## Notes
+
+- Markdown output quality depends on source file quality.
+- For large batches, convert in chunks and review failures file-by-file.
+- For OCR/transcription workloads, install optional extras (`[all]`) via `setup-markitdown`.

package/app/out/skills/community-builtin/markitdown/scripts/batch-convert.sh

@@ -0,0 +1,40 @@
+#!/usr/bin/env bash
+set -euo pipefail
+
+if [ "$#" -lt 2 ]; then
+  echo "Usage: batch-convert.sh <input-dir> <output-dir>" >&2
+  exit 1
+fi
+
+INPUT_DIR="$1"
+OUTPUT_DIR="$2"
+
+mkdir -p "$OUTPUT_DIR"
+
+if command -v markitdown >/dev/null 2>&1; then
+  MARKITDOWN_CMD=(markitdown)
+elif python3 -c "import markitdown" >/dev/null 2>&1; then
+  MARKITDOWN_CMD=(python3 -m markitdown)
+else
+  UV_CACHE_DIR="${UV_CACHE_DIR:-$PWD/.agentfoundry/cache/uv-cache}"
+  UV_TOOL_DIR="${UV_TOOL_DIR:-$PWD/.agentfoundry/cache/uv-tools}"
+  mkdir -p "$UV_CACHE_DIR" "$UV_TOOL_DIR"
+  MARKITDOWN_CMD=(env UV_CACHE_DIR="$UV_CACHE_DIR" UV_TOOL_DIR="$UV_TOOL_DIR" uvx --from "markitdown[all]" markitdown)
+fi
+
+find "$INPUT_DIR" -type f | while IFS= read -r source_file; do
+  rel_path="${source_file#"$INPUT_DIR"/}"
+  file_stem="$(basename "$rel_path")"
+  file_stem="${file_stem%.*}"
+  out_dir="$OUTPUT_DIR/$(dirname "$rel_path")"
+  out_file="$out_dir/$file_stem.md"
+
+  mkdir -p "$out_dir"
+  echo "converting: $source_file -> $out_file"
+
+  "${MARKITDOWN_CMD[@]}" "$source_file" -o "$out_file" || {
+    echo "warning: failed to convert $source_file" >&2
+  }
+done
+
+echo "batch conversion complete: $INPUT_DIR -> $OUTPUT_DIR"

package/app/out/skills/community-builtin/markitdown/scripts/convert-file.sh

@@ -0,0 +1,24 @@
+#!/usr/bin/env bash
+set -euo pipefail
+
+if [ "$#" -lt 2 ]; then
+  echo "Usage: convert-file.sh <input-file> <output-md>" >&2
+  exit 1
+fi
+
+INPUT_PATH="$1"
+OUTPUT_PATH="$2"
+
+if command -v markitdown >/dev/null 2>&1; then
+  markitdown "$INPUT_PATH" -o "$OUTPUT_PATH"
+elif python3 -c "import markitdown" >/dev/null 2>&1; then
+  python3 -m markitdown "$INPUT_PATH" -o "$OUTPUT_PATH"
+else
+  UV_CACHE_DIR="${UV_CACHE_DIR:-$PWD/.agentfoundry/cache/uv-cache}"
+  UV_TOOL_DIR="${UV_TOOL_DIR:-$PWD/.agentfoundry/cache/uv-tools}"
+  mkdir -p "$UV_CACHE_DIR" "$UV_TOOL_DIR"
+  env UV_CACHE_DIR="$UV_CACHE_DIR" UV_TOOL_DIR="$UV_TOOL_DIR" \
+    uvx --from "markitdown[all]" markitdown "$INPUT_PATH" -o "$OUTPUT_PATH"
+fi
+
+echo "converted: $INPUT_PATH -> $OUTPUT_PATH"

package/app/out/skills/community-builtin/markitdown/scripts/setup-markitdown.sh

@@ -0,0 +1,10 @@
+#!/usr/bin/env bash
+set -euo pipefail
+
+if command -v uv >/dev/null 2>&1; then
+  uv pip install "markitdown[all]"
+else
+  python3 -m pip install --user "markitdown[all]"
+fi
+
+echo "markitdown installation completed"

package/app/out/skills/community-builtin/repo-quick-audit/SKILL.md

@@ -0,0 +1,27 @@
+---
+id: repo-quick-audit
+name: Repo Quick Audit
+shortDescription: Fast local repository sanity checks
+loadingStrategy: lazy
+tools:
+  - skill-script-run
+tags:
+  - community
+  - audit
+meta:
+  approvedByUser: true
+---
+
+# Summary
+Run a fast repository audit with `skill-script-run` before deep debugging.
+
+## Procedures
+1. Run script `audit-basics` to collect quick health signals.
+2. Review output for dirty git state, TODO count, and unresolved merge markers.
+3. If warnings exist, prioritize fixes before adding new features.
+
+## Examples
+- `skill-script-run` with `{ "skillId": "repo-quick-audit", "script": "audit-basics" }`
+
+## Troubleshooting
+- If script output is empty, run from project root (`cwd: "."`).

package/app/out/skills/community-builtin/repo-quick-audit/scripts/audit-basics.sh

@@ -0,0 +1,19 @@
+#!/usr/bin/env bash
+set -euo pipefail
+
+echo "[audit] git status"
+git status --short || true
+
+echo "[audit] todo count"
+if command -v rg >/dev/null 2>&1; then
+  rg --glob '!node_modules/**' --glob '!.git/**' "TODO|FIXME" . | wc -l | awk '{print $1}'
+else
+  grep -R --exclude-dir=node_modules --exclude-dir=.git -E "TODO|FIXME" . | wc -l | awk '{print $1}'
+fi
+
+echo "[audit] merge markers"
+if command -v rg >/dev/null 2>&1; then
+  rg --glob '!node_modules/**' --glob '!.git/**' "^(<<<<<<<|=======|>>>>>>>)" . || true
+else
+  grep -R --exclude-dir=node_modules --exclude-dir=.git -E "^(<<<<<<<|=======|>>>>>>>)" . || true
+fi

package/app/out/skills/research-pilot-default-project-skills/README.md

@@ -0,0 +1,23 @@
+# Research Pilot Default Project Skills
+
+These skills are application-specific defaults for Research Pilot.
+
+Directory layout:
+
+```text
+examples/research-pilot/skills/default-project-skills/<skill-id>/SKILL.md
+examples/research-pilot/skills/default-project-skills/<skill-id>/scripts/*
+```
+
+Included skills:
+- `citation-management`
+- `research-grants`
+- `matplotlib`
+
+Desktop startup seeds these into each opened project at:
+
+```text
+.agentfoundry/skills/<skill-id>
+```
+
+Seeding is non-destructive: existing project-local skills are not overwritten.