bugfixes

.gitignore

@@ -1,3 +1,13 @@
 nvim/snapshot
 nvim/plugin
 nvim/nvim
+nvim/lazy-lock.json
+
+gemini/history
+gemini/tmp
+gemini/google_accounts.json
+gemini/installation_id
+gemini/oauth_creds.json
+gemini/projects.json
+gemini/state.json
+gemini/trustedFolders.json

GEMINI.md

@@ -0,0 +1,54 @@
+# Dotfiles Project Overview
+
+This repository contains personal configuration files (dotfiles) for various tools, including Zsh, Neovim, Tmux, Git, and more. It is designed to be portable across macOS (Darwin) and Linux (Debian-based distributions).
+
+## Core Technologies
+- **Shell:** Zsh with [Oh My Zsh](https://ohmyz.sh/), [ys theme](https://github.com/ohmyzsh/ohmyzsh/wiki/Themes#ys), and several plugins (`gh`, `git`, `vi-mode`, `pyenv`, `nodenv`, `asdf`, `poetry`).
+- **Editor:** Neovim configured using [LazyVim](https://www.lazyvim.org/) and [lazy.nvim](https://github.com/folke/lazy.nvim).
+- **Terminal Multiplexer:** Tmux with platform-specific configurations (`tmux/Darwin.conf` and `tmux/Linux.conf`).
+- **Tool Managers:** Supports `pyenv`, `nodenv`, `rbenv`, `goenv`, `tfenv`, and `rustup`.
+- **Package Managers:** Homebrew (macOS) and `apt` (Linux).
+
+## Directory Structure
+- `bin/`: Custom scripts and binaries.
+- `nvim/`: Neovim configuration (`init.lua`, `lua/config/`, `lua/plugins/`).
+- `shlibs/`: Shell libraries for installation, logging, and environment detection.
+- `tmux/`: Tmux configurations, including OS-specific overrides.
+- `zsh/`: Zsh environment, aliases, functions, and SSH agent setup.
+- `install.sh`: The main installation script for dependencies and configuration linking.
+
+## Building and Running
+
+### Installation
+The primary entry point for setting up the environment is `install.sh`.
+
+```bash
+# General installation (deps + config)
+./install.sh install
+
+# Only install configurations (symlinking)
+./install.sh config
+
+# Fast installation (skips some prompts)
+./install.sh fast-install
+
+# Install only Neovim and its dependencies
+./install.sh install-neovim
+```
+
+The `install.sh` script performs the following actions:
+1. Installs system-level dependencies via Homebrew or `apt`.
+2. Sets up tool version managers (`pyenv`, `nodenv`, etc.).
+3. Installs Rust, Neovim, and various CLI tools (`ripgrep`, `fd`, `gh`).
+4. Symlinks configuration files from the repository to the home directory (e.g., `~/.zshrc`, `~/.tmux.conf`, `~/.config/nvim`).
+
+### Maintenance
+- **Purge configurations:** `./install.sh purge` removes the symlinks created by the installer.
+- **Update Neovim:** The installer includes a `compile_neovim` function for Linux environments to build from source.
+
+## Development Conventions
+
+- **Shell Scripting:** Shared logic is modularized in `shlibs/`. Use `shlibs/logging.sh` for output and `shlibs/os.sh` for platform detection.
+- **Neovim Configuration:** Follows the `LazyVim` structure. Custom plugins should be added to `nvim/lua/plugins/`, and core configurations to `nvim/lua/config/`.
+- **Environment Variables:** Managed in `zsh/env.zsh`. Paths and tool initializations should be added there to ensure they are available in the shell.
+- **Aliases:** Custom aliases are located in `zsh/aliases.zsh`.

gemini/GEMINI.md

@@ -0,0 +1,15 @@
+
+# Use Tools available
+use mcp_context7_query-docs to query for api documentation
+use mcp_github for relevant github tasks
+use mcp_astgrep for abstract syntax tree dumps and efficient structured code search
+
+# Making changes
+- break down commits by units of work
+- commits should be broken down into logical parts
+- do not group unrelated changes into a single commit
+- do not comment code.
+- code should be self documenting.
+- use clear naming, descriptive variables.
+- code should prioritize readability
+- code should be concise, but not obfuscated.

gemini/policies/tools.toml

@@ -0,0 +1,167 @@
+# Project-level tool permissions migrated from tools.allowed and tools.exclude
+# Generated to comply with Gemini CLI 1.0 Policy Engine migration.
+
+# Allowed shell commands (No-prompt)
+[[rule]]
+toolName = "run_shell_command"
+commandPrefix = "git status"
+decision = "allow"
+priority = 100
+
+[[rule]]
+toolName = "run_shell_command"
+commandPrefix = "git diff"
+decision = "allow"
+priority = 100
+
+[[rule]]
+toolName = "run_shell_command"
+commandPrefix = "git log"
+decision = "allow"
+priority = 100
+
+[[rule]]
+toolName = "run_shell_command"
+commandPrefix = "git grep"
+decision = "allow"
+priority = 100
+
+[[rule]]
+toolName = "run_shell_command"
+commandPrefix = "git branch --show-current"
+decision = "allow"
+priority = 100
+
+[[rule]]
+toolName = "run_shell_command"
+commandPrefix = "git remote -v"
+decision = "allow"
+priority = 100
+
+[[rule]]
+toolName = "run_shell_command"
+commandPrefix = "gh pr status"
+decision = "allow"
+priority = 100
+
+[[rule]]
+toolName = "run_shell_command"
+commandPrefix = "gh show"
+decision = "allow"
+priority = 100
+
+[[rule]]
+toolName = "run_shell_command"
+commandPrefix = "gh pr checks"
+decision = "allow"
+priority = 100
+
+[[rule]]
+toolName = "run_shell_command"
+commandPrefix = "gh pr view"
+decision = "allow"
+priority = 100
+
+[[rule]]
+toolName = "run_shell_command"
+commandPrefix = "gh run view"
+decision = "allow"
+priority = 100
+
+[[rule]]
+toolName = "run_shell_command"
+commandPrefix = "diff"
+decision = "allow"
+priority = 100
+
+[[rule]]
+toolName = "run_shell_command"
+commandPrefix = "find"
+decision = "allow"
+priority = 100
+
+[[rule]]
+toolName = "run_shell_command"
+commandPrefix = "pwd"
+decision = "allow"
+priority = 100
+
+[[rule]]
+toolName = "run_shell_command"
+commandPrefix = "grep"
+decision = "allow"
+priority = 100
+
+[[rule]]
+toolName = "run_shell_command"
+commandPrefix = "cat"
+decision = "allow"
+priority = 100
+
+[[rule]]
+toolName = "run_shell_command"
+commandPrefix = "ls"
+decision = "allow"
+priority = 100
+
+[[rule]]
+toolName = "run_shell_command"
+commandPrefix = "poetry run flake8"
+decision = "allow"
+priority = 100
+
+[[rule]]
+toolName = "run_shell_command"
+commandPrefix = "poetry run pyright"
+decision = "allow"
+priority = 100
+
+[[rule]]
+toolName = "run_shell_command"
+commandPrefix = "cd"
+decision = "allow"
+priority = 100
+
+# Other allowed tools
+[[rule]]
+toolName = "find_code"
+decision = "allow"
+priority = 100
+
+[[rule]]
+toolName = "list_directory"
+decision = "allow"
+priority = 100
+
+[[rule]]
+toolName = "read_file"
+decision = "allow"
+priority = 100
+
+# Explicitly allowed git commands for specific repositories
+# Uses argsPattern to match both the command and the dir_path (keys are sorted alphabetically)
+[[rule]]
+toolName = "run_shell_command"
+argsPattern = '"command":"git (add|commit|push|pull|fetch|rebase|reset|stash|status|diff|log|grep).*","dir_path":"/.*/repos/jaybocc2/.*"'
+decision = "allow"
+priority = 120
+
+[[rule]]
+toolName = "run_shell_command"
+commandPrefix = "git commit"
+decision = "ask_user"
+priority = 100
+
+[[rule]]
+toolName = "run_shell_command"
+commandPrefix = "git add"
+decision = "ask_user"
+priority = 100
+
+# Explicitly denied shell commands
+[[rule]]
+toolName = "run_shell_command"
+commandPrefix = "git push"
+decision = "deny"
+priority = 100
+deny_message = "Git push is restricted by project policy. Please use git commands directly if needed."

gemini/settings.json

@@ -1,6 +1,12 @@
 {
-  "selectedAuthType": "oauth-personal",
-  "preferredEditor": "neovim",
+  "policyPaths": [
+    "./gemini/policies"
+  ],
+  "security": {
+    "auth": {
+      "selectedType": "oauth-personal"
+    }
+  },
   "checkpointing": {
     "enabled": true
   },
@@ -20,17 +26,64 @@
       ]
     },
     "github": {
+      "description": "Connect AI assistants to GitHub - manage repos, issues, PRs, and workflows through natural language.",
       "httpUrl": "https://api.githubcopilot.com/mcp/",
       "headers": {
-        "Authorization": "${GITHUB_PAT}"
+        "Authorization": "Bearer ${GITHUB_PAT}"
       },
       "timeout": 5000
     },
     "context7": {
+      "description": "Up-to-date code docs for any prompt",
       "httpUrl": "https://mcp.context7.com/mcp",
       "headers": {
         "CONTEXT7_API_KEY": "${CONTEXT7_API_KEY}"
       }
     }
+  },
+  "context": {
+    "fileName": [
+      "AGENTS.md",
+      "CONTEXT.md",
+      "GEMINI.md",
+      "CLAUDE.md",
+      ".claude/CLAUDE.md"
+    ]
+  },
+  "tools": {
+    "core": [
+      "list_directory",
+      "read_file",
+      "grep_search",
+      "glob",
+      "replace",
+      "write_file",
+      "web_fetch",
+      "run_shell_command",
+      "save_memory",
+      "google_web_search",
+      "ask_user",
+      "codebase_investigator",
+      "cli_help",
+      "activate_skill"
+    ]
+  },
+  "general": {
+    "preferredEditor": "neovim",
+    "sessionRetention": {
+      "enabled": true,
+      "maxAge": "30d",
+      "warningAcknowledged": true
+    }
+  },
+  "experimental": {
+    "plan": true
+  },
+  "vimMode": true,
+  "fileFiltering": {
+    "respectGitIgnore": true
+  },
+  "model": {
+    "name": "auto-gemini-3"
   }
-}
+}

gemini/skills/address-pr-feedback/SKILL.md

@@ -0,0 +1,61 @@
+---
+name: address-pr-comments
+description: Address review comments on a GitHub pull request. Use when the user asks to "address PR comments", "respond to review feedback", "handle reviewer comments", or "resolve review threads".
+disable-model-invocation: true
+---
+
+# Address PR Review Comments
+
+## Context
+
+- Current branch: !`git branch --show-current`
+- get pull request review with git mcp: `pull_request_read`
+
+## Your task
+
+Work through every unresolved review thread on this PR systematically. For each thread:
+
+### Step 1 — Understand the comment
+Read the comment carefully. Identify:
+- What file and line it refers to
+- What the reviewer is asking for (change, question, clarification, nitpick)
+- Whether a code change is actually required
+
+### Step 2 — Make changes if needed
+If a code change is warranted:
+- Read the relevant file(s) first
+- Make the change using Edit (or Write for new files)
+- Do NOT commit yet — collect all changes first
+
+If no change is needed (e.g. the reviewer asked a question, or you disagree), prepare a clear explanation.
+
+### Step 3 — Commit each change separately
+After addressing a comment that requires code changes, create a single follow-up commit. Write a short message that summarizes what was changed (e.g. `"fix: use const for immutable bindings per review"`) rather than a generic message:
+
+Skip this step if no code changes were made.
+Provide a commit message and wait until prompted to continue if not allowed by policy to commit.
+
+### Step 4 — Reply to each comment
+use github mcp
+
+Good reply patterns:
+- For changes made: "Done — <brief description of what changed>."
+- For questions answered: "< direct answer to question >."
+- For declined suggestions: "I kept the existing approach because <reason>."
+- For issues already resolved in code: "I fixed this in <commit>"
+
+### Step 5 — Resolve each thread
+Resolve every thread/comment if satisfactory
+use git mcp / gh cli and GraphQL id field:
+
+```
+gh api graphql -f query='mutation { resolveReviewThread(input: {threadId: "<thread_id>"}) { thread { id isResolved } } }'
+```
+## Notes
+
+- break down commits by units of work
+- commits should be broken down into logical parts
+- do not group unrelated changes into a single commit
+- If the PR has no open review threads, report that there is nothing to address
+- Always reply before resolving so the reviewer sees the response
+- Keep replies concise and direct