The fix in commit 215a618 for issue #2096 introduced an O(n^2) time
complexity regression when projects have multiple source folders
sharing the same output location (like SWT with 26 source roots).

The problem was that each source folder caused a new CompositeApiTypeContainer
to be created, wrapping all previous containers plus a new one. This
resulted in exponential duplication of container visits during API analysis.

The fix modifies ProjectTypeContainer to support multiple
IPackageFragmentRoots, allowing a single container to discover packages
from all source folders that share the same output location. This avoids
creating composite containers and maintains O(n) complexity.

Fixes #2197

Signed-off-by: moaead <moaead@users.noreply.github.com>