chore: tidy repo root + .gitignore to match OpenResearcher-style layout

[reacher-z]

Goal

Tidy the repo so a first-time visitor (and a fresh git clone) sees a clean,
purposeful layout — closer to TIGER-AI-Lab/OpenResearcher,
whose root is just README.md, pyproject.toml, .gitignore,
.env.template, a few top-level modules, and assets/ + scripts/ + utils/.

Our committed root is already reasonable, but a few things have crept in that
make the project look less polished than it is. None of this touches behavior —
it's pure hygiene.

Checklist

1. Stop tracking .env (priority)

.env is currently committed. It should never be in version control:

• git rm --cached .env, commit a .env.template with keys only, no values
• add .env to .gitignore
• rotate any real credentials that were ever committed and purge the file from history (git filter-repo / BFG) — anything that lived in a public repo must be treated as compromised
• document required env vars in the README / .env.template

2. Expand .gitignore so git status is clean on a fresh checkout

Right now a clone picks up a lot of scratch noise that isn't ignored. Add:

• .env
• ._* (macOS AppleDouble files)
• *.bak, *.bak.*
• root scratch screenshots (/*.png) — keep intentional images under assets/ (see Rename .env.example to .env with PurelyMail config #3)
• one-off session transcripts (*-this-session-*.txt and similar)
• ad-hoc analysis scripts that aren't part of the package (or move them — see Add Chinese README and language switcher #5)

3. Put images in assets/

Mirror OpenResearcher's assets/ dir — move README/figure images there and
reference them via relative paths, instead of leaving screenshots loose.

4. Consolidate non-standard root docs into docs/

docs/ currently holds only v1-vs-v2.md. Move project-internal docs there to
slim the root:

• AGENTS.md → docs/
• CHANGELOG.md → docs/ (or keep at root — maintainer's call)
• keep the GitHub-convention root files as-is: README.md, README.zh-CN.md, LICENSE, NOTICE, CITATION.cff, CONTRIBUTING.md

5. Collect loose scripts under scripts/

Match OpenResearcher's scripts/ + utils/ split — move stray top-level shell
/ analysis scripts into scripts/, leaving only the documented entrypoints
(run.sh) at root.

Acceptance

• git status on a fresh clone is empty (no untracked cruft)
• root tree is close to OpenResearcher's: README + standard files + src/ docs/ eval/ assets/ scripts/ tests/
• no secrets tracked anywhere in history

[Perry2004]

• .env is intentionally committed.
• AGENTS.md and CHANGELOG.md are placed at the root by convention.
• The source code maintains the standard Python package structure since we need to build & publish to PyPI.
• Rests are addressed in Cleanup repo root #202 #203