Fix PDM settings ignoring PDM's config layers (#609, #566) (#611)

* Start fix for #609, #566

Assisted-by: Claude Code:claude-opus-5-5

* Read PDM settings through PDM's config layers

Agent mode decided whether a PDM project uses PEP 582
(__pypackages__) from the project's pdm.toml alone, and only when
use_venv was a TOML bool. PDM 2.27+ writes `use_venv = "false"`, and
plain `pdm config python.use_venv false` writes the user config, so
socket-patch patched an activated or stray venv instead of the copy
`pdm run` imports (#609).

Global mode likewise skipped PDM's site config
(/etc/xdg/pdm/config.toml and the macOS/Windows equivalents), so a
global project relocated there was never crawled and `get -g` could
patch a different copy (#566).

Settings now resolve in PDM's order: environment, project config,
user config ($PDM_CONFIG_FILE or the per-user file), then the site
config, with string values parsed like PDM's ensure_boolean.

Assisted-by: Claude Code:claude-opus-5-5

* Read one PDM user config, skip empty XDG dirs

PDM reads a single user config file: the most specific per-user
config dir platformdirs picks. A use_venv missing from
$XDG_CONFIG_HOME/pdm/config.toml no longer falls through to
~/.config/pdm, which PDM never reads in that setup.

A leading empty or relative $XDG_CONFIG_DIRS entry (e.g. from
"$XDG_CONFIG_DIRS:/other" with the variable unset) no longer drops
the site config layer. The first absolute entry is used, falling
back to /etc/xdg.

Assisted-by: Claude Code:claude-opus-5-5

* Match PDM project precedence and macOS site config

Honor XDG_CONFIG_DIRS for macOS site defaults and preserve native root/whitespace handling. Overlay legacy project settings before modern pdm.toml, while retaining environment priority and missing-key fallback. Enable site-layer tests on macOS and cover both legacy/string directions.

Validation: 68 Python crawler tests passed; native PDM 2.29.2 controls with platformdirs 4.9.6 and 4.12.2. The legacy regression also passes on main and fails with the original PR lookup.

* Resolve implicit PDM site config with its macOS runtime

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Co-authored-by: Claude <noreply@anthropic.com>

Author: mikolalysenko