Upgrade Feynman research runtime and setup

README.md

@@ -9,12 +9,14 @@ It keeps the useful parts of a coding agent:
 - skills
 - custom extensions
 
-But it biases the runtime toward research work:
+But it biases the runtime toward general research work:
 - literature review
-- paper lookup
+- source discovery and paper lookup
 - source comparison
 - research memo writing
 - paper and report drafting
+- session recall and durable research memory
+- recurring and deferred research jobs
 - replication planning when relevant
 
 The primary paper backend is `@companion-ai/alpha-hub` and your alphaXiv account.
@@ -29,7 +31,7 @@ npm install -g @companion-ai/feynman
 Then authenticate alphaXiv and start the CLI:
 
 ```bash
-feynman --alpha-login
+feynman setup
 feynman
 ```
 
@@ -43,7 +45,12 @@ npm run start
 ```
 
 Feynman uses Pi under the hood, but the user-facing entrypoint is `feynman`, not `pi`.
-When you run `feynman`, it launches the real Pi interactive TUI with Feynman's research extensions, skills, prompts, and package stack preloaded.
+When you run `feynman`, it launches the real Pi interactive TUI with Feynman's research extensions, skills, prompts, package stack, memory snapshot, and branded defaults preloaded.
+
+Most users should not need slash commands. The intended default is:
+- ask naturally
+- let Feynman route into the right workflow
+- use slash commands only as explicit shortcuts or overrides
 
 ## Commands
 
@@ -56,10 +63,19 @@ Inside the REPL:
 - `/replicate <paper or claim>` expands the replication prompt template
 - `/reading-list <topic>` expands the reading-list prompt template
 - `/research-memo <topic>` expands the general research memo prompt template
+- `/deepresearch <topic>` expands the thorough source-heavy research prompt template
+- `/autoresearch <idea>` expands the end-to-end idea-to-paper prompt template
 - `/compare-sources <topic>` expands the source comparison prompt template
 - `/paper-code-audit <item>` expands the paper/code audit prompt template
 - `/paper-draft <topic>` expands the paper-style writing prompt template
-- `/research-memo <topic>` expands the general research memo prompt template
+
+Outside the REPL:
+
+- `feynman setup` configures alpha login, web research, and preview deps
+- `feynman --alpha-login` signs in to alphaXiv
+- `feynman --alpha-status` checks alphaXiv auth
+- `feynman --doctor` checks models, auth, preview dependencies, and branded settings
+- `feynman --setup-preview` installs `pandoc` automatically on macOS/Homebrew systems when preview support is missing
 
 ## Custom Tools
 
@@ -71,6 +87,8 @@ The starter extension adds:
 - `alpha_annotate_paper` for persistent local notes
 - `alpha_list_annotations` for recall across sessions
 - `alpha_read_code` for reading a paper repository
+- `session_search` for recovering prior Feynman work from stored transcripts
+- `preview_file` for browser/PDF review of generated artifacts
 
 Feynman uses `@companion-ai/alpha-hub` directly in-process rather than shelling out to the CLI.
 
@@ -82,10 +100,16 @@ Feynman loads a lean research stack from [.pi/settings.json](/Users/advaitpaliwa
 - `pi-docparser` for PDFs, Office docs, spreadsheets, and images
 - `pi-web-access` for broader web, GitHub, PDF, and media access
 - `pi-markdown-preview` for polished Markdown and LaTeX-heavy research writeups
+- `@walterra/pi-charts` for charts and quantitative visualizations
+- `pi-generative-ui` for interactive HTML-style widgets
+- `pi-mermaid` for diagrams in the TUI
 - `@aliou/pi-processes` for long-running experiments and log tails
 - `pi-zotero` for citation-library workflows
+- `@kaiserlich-dev/pi-session-search` for indexed session recall and summarize/resume UI
+- `pi-schedule-prompt` for recurring and deferred research jobs
+- `@samfp/pi-memory` for automatic preference/correction memory across sessions
 
-The default expectation is source-grounded outputs with explicit `Sources` sections containing direct URLs.
+The default expectation is source-grounded outputs with explicit `Sources` sections containing direct URLs and durable artifacts written to `outputs/`, `notes/`, `experiments/`, or `papers/`.
 
 ## Layout
 
@@ -95,5 +119,5 @@ feynman/
 ├── papers/       # Polished paper-style drafts and writeups
 ├── prompts/      # Slash-style prompt templates
 ├── skills/       # Research workflows
-└── src/          # Minimal REPL wrapper around pi-coding-agent
+└── src/          # Branded launcher around the embedded Pi TUI
 ```