fix(mcp): restore uninit/placeholder/filled split in getProjectSoul

The compare/overwrite UI reverted the previous improvement to this method
(commit 8eb6c3db) and dropped the bootstrap guidance for fresh customers.
Re-applied: differentiate 'no .axis/ directory yet' (point at
`npx @virsanghavi/axis-init`) from 'placeholder content' (call
update_project_soul) so a brand-new project doesn't drop the agent into
the same generic 'soul is not yet filled' message regardless of how
unfinished the install actually is.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>