If you want overlay eclasses to override eclasses from other repos then you'll want to refer to the portage(5) man page for information about the /etc/portage/repos.conf file which can be used to specify site-specific repository configuration information. Note that configuration settings which are specified in repos.conf do not apply to tools such as repoman(1) and egencache(1), since operations performed by these tools are inherently not site-specific.

Since portage-2.2_rc31, repos.conf can be used to create repository aliases, in case you want to substitute one repo for another one that is specified in layout.conf. This is especially useful for funtoo users, who may want something like this in /etc/portage/repos.conf:

[funtoo]
aliases = gentoo

Calculating dependencies... done!
[ebuild  N    ] sys-libs/e2fsprogs-libs-1.41.3-r1  USE="nls"
[ebuild     U ] sys-fs/e2fsprogs-1.41.3 [1.40.9]
[blocks b     ] <sys-fs/e2fsprogs-1.41 ("<sys-fs/e2fsprogs-1.41" is blocking sys-libs/e2fsprogs-libs-1.41.3-r1)
[blocks B     ] sys-libs/com_err ("sys-libs/com_err" is blocking sys-libs/e2fsprogs-libs-1.41.3-r1)
[blocks B     ] sys-libs/ss ("sys-libs/ss" is blocking sys-libs/e2fsprogs-libs-1.41.3-r1)
[blocks B     ] sys-libs/e2fsprogs-libs ("sys-libs/e2fsprogs-libs" is blocking sys-libs/com_err-1.40.9, sys-libs/ss-1.40.9)

 * Error: The above package list contains packages which cannot be
 * installed at the same time on the same system.

  ('installed', '/', 'sys-libs/com_err-1.40.9', 'nomerge') pulled in by
    ~sys-libs/com_err-1.40.9 required by ('installed', '/', 'sys-libs/ss-1.40.9', 'nomerge')

  ('installed', '/', 'sys-libs/ss-1.40.9', 'nomerge') pulled in by
    sys-libs/ss required by world

  ('ebuild', '/', 'sys-libs/e2fsprogs-libs-1.41.3-r1', 'merge') pulled in by
    >=sys-libs/e2fsprogs-libs-1.41 required by ('installed', '/', 'sys-apps/util-linux-2.14.1', 'nomerge')
    ~sys-libs/e2fsprogs-libs-1.41.3 required by ('ebuild', '/', 'sys-fs/e2fsprogs-1.41.3', 'merge')

The above output shows that the sys-libs/ss package got pulled into the dependency graph by the world set. This package is obsolete, so the user should remove it from /var/lib/portage/world. In the future, I plan to add support for emerge to ask the user if they'd like to have the obsolete package automatically removed from the world file (bug 257009).

# Installed ebuilds that inherit from known live eclasses.
[live-rebuild]
class = portage.sets.dbapi.InheritSet
world-candidate = False
inherits = cvs darcs git mercurial subversion

# Installed packages that own files inside /lib/modules.
[module-rebuild]
class = portage.sets.dbapi.OwnerSet
world-candidate = False
files = /lib/modules

Given the new InheritSet and OwnerSet classes, it's easy to define similar sets based on inherited eclasses and installed files, respectively.

For more information about experimental EAPI features, refer to bug #233213 and also see the "Ebuild" chapter of the html documentation that is installed with portage when USE=doc is enabled. I've posted a copy of the EAPI="2_pre1" documentation here:

EAPI 2_pre1

  Helpers

    doman

      Language codes in file names are now used for path translation.

      Table 6.1. Man Page Path Translation

        Source        Destination
        foo.1         /usr/share/man/man1/foo.1
        foo.lang.1    /usr/share/man/lang/man1/foo.1

  USE Dependencies

    Unconditional USE Dependencies

      Table 6.2. Syntax Examples

        Example          Meaning
        foo[bar]         foo must have bar enabled
        foo[bar,baz]     foo must have both bar and baz enabled
        foo[-bar,baz]    foo must have bar disabled and baz enabled

    Conditional USE Dependencies

      Table 6.3. Syntax Examples

        Compact Form    Equivalent Expanded Form
        foo[bar?]       bar? ( foo[bar]  ) !bar? ( foo       )
        foo[!bar?]      bar? ( foo       ) !bar? ( foo[-bar] )
        foo[bar=]       bar? ( foo[bar]  ) !bar? ( foo[-bar] )
        foo[!bar=]      bar? ( foo[-bar] ) !bar? ( foo[bar]  )

--jobs JOBS
	Specifies the number of packages to build simultaneously.
	Also see the related --load-average option.

--keep-going
	Continue as much as possible after an error. When an error
	occurs, dependencies are recalculated for remaining packages
	and any with unsatisfied dependencies are automatically
	dropped. Also see the related --skipfirst option.

--load-average LOAD
	Specifies that no new builds should be started if there are
	other builds running and the load average is at least LOAD (a
	floating-point number). This option is recommended for use in
	combination with --jobs in order to avoid excess load. See
	make(1) for information about analogous options that should
	be configured via MAKEOPTS in make.conf(5).

Here is some sample parallel build output from a catalyst stage2 build, with emerge's new --jobs option enabled:

>>> Building (1 of 10) sys-devel/gettext-0.17 for /
>>> Building (2 of 10) sys-libs/zlib-1.2.3-r1 for /
>>> Building (3 of 10) virtual/libintl-0 for /
>>> Building (4 of 10) dev-util/unifdef-1.20 for /
>>> Installing virtual/libintl-0 to /
>>> Installing dev-util/unifdef-1.20 to /
>>> Building (5 of 10) sys-kernel/linux-headers-2.6.23-r3 for /
>>> Installing sys-libs/zlib-1.2.3-r1 to /
>>> Jobs: 3 of 10 complete, 2 running               Load avg: 3.44, 1.46, 0.69

If one package blocks another package, the two packages conflict such that they cannot be installed simultaneously. These conflicts are often due to file collisions. In some cases, packages that block each other can be temporarily installed simultaneously. In order to resolve file collisions that occur between two blocking packages that are installed simultaneously, the overlapping files must be removed from the contents list of the package which was installed first.

Some cases may exist such that temporary simultaneous installation of blocking packages will cause some sort of problem. However, this type of solution will only be chosen for blockers that can not be satisfied in any other way, such as by simple adjustment of merge order. In addition, this type of solution will not be chosen if a blocking package will overwrite files belonging to packages from the system set, or packages that are runtime dependencies of Portage itself. These constraints serve to limit the probability that a chosen solution will cause an unforeseen problem.

gtk-doc-am vs. gtk-doc-1.8-r2

These are the packages that would be merged, in reverse order:

Calculating dependencies... done!
[blocks b     ] dev-util/gtk-doc-am (is blocking dev-util/gtk-doc-1.8-r2)
[uninstall    ]  dev-util/gtk-doc-1.8-r2  USE="emacs -debug -doc"
[nomerge      ] x11-libs/gtk+-2.12.9-r2  USE="X cups jpeg tiff xinerama -debug -doc -vim-syntax"
[ebuild  N    ]  dev-util/gtk-doc-am-1.10-r1  0 kB

Total: 1 package (1 new, 1 uninstall), Size of downloads: 0 kB
Conflict: 1 block

coreutils vs. mktemp

These are the packages that would be merged, in reverse order:

Calculating dependencies... done!
[nomerge      ] sys-apps/coreutils-6.11 [6.9-r1] USE="acl nls xattr (-selinux) -static -vanilla%"
[blocks b     ]  sys-apps/mktemp (is blocking sys-apps/coreutils-6.11)
[blocks b     ] >=sys-apps/coreutils-6.10 (is blocking sys-apps/mktemp-1.5)
[uninstall    ]  sys-apps/mktemp-1.5
[ebuild     U ] sys-apps/coreutils-6.11 [6.9-r1] USE="acl nls xattr (-selinux) -static -vanilla%" 0 kB

Total: 1 package (1 upgrade, 1 uninstall), Size of downloads: 0 kB
Conflict: 2 blocks

gtk-doc-am vs. gtk-doc-1.8-r2

These are the packages that would be merged, in reverse order:

Calculating dependencies... done!
[nomerge      ] x11-libs/gtk+-2.12.9-r2  USE="X cups jpeg tiff xinerama -debug -doc -vim-syntax"
[ebuild  N    ]  dev-util/gtk-doc-am-1.10-r1  0 kB
[blocks b     ] dev-util/gtk-doc-am (is blocking dev-util/gtk-doc-1.8-r2)
[uninstall    ]  dev-util/gtk-doc-1.8-r2  USE="emacs -debug -doc"

Total: 1 package (1 new, 1 uninstall), Size of downloads: 0 kB
Conflict: 1 block

coreutils vs. mktemp

These are the packages that would be merged, in reverse order:

Calculating dependencies... done!
[ebuild     U ] sys-apps/coreutils-6.11 [6.9-r1] USE="acl nls xattr (-selinux) -static -vanilla%" 0 kB
[blocks b     ]  sys-apps/mktemp (is blocking sys-apps/coreutils-6.11)
[blocks b     ] >=sys-apps/coreutils-6.10 (is blocking sys-apps/mktemp-1.5)
[uninstall    ]  sys-apps/mktemp-1.5

Total: 1 package (1 upgrade, 1 uninstall), Size of downloads: 0 kB
Conflict: 2 blocks

Portage Dependency Resolution - Decision Making

Dependency Expression Evaluation

In terms of boolean logic, a dependency expression can
be expressed in disjunctive normal form (DNF), which is a
disjunction of conjunctive clauses. Each conjunctive clause
represents one possible alternative combination of dependency
atoms capable of satisfying the dependency expression.

Look-Ahead

When there are multiple combinations to choose from, a
look-ahead mechanism will choose an optimal combination to
satisfy constraints and minimize cost. The following package
states influence the cost calculation for a given combination:

• installed
• selected (for installation)
• not selected (for installation)

In cost calculations, virtual packages by themselves are
considered to cost nothing since they do not directly install
anything. It is the dependencies of a virtual package that
contribute to it's cost.

Constraint Propagation

Combinations that include packages from the "installed" or
"selected" categories are less costly than those that include
packages from the "not selected" category. When a package
is chosen for installation, it transitions to the "selected"
state. This state change propagates to the cost calculations of
later decisions, influencing later decisions to be consistent
with earlier decisions. This feedback mechanism serves to
propagate constraints and can influence the modeling process
to converge on a more optimal final state.

Expanded Search Space

When evaluating virtual atoms, an expanded search space is
considered which recursively traverses the dependencies of
virtual packages from all slots matching a given virtual
atom. All combinations in this expanded search space are
considered when choosing an optimal combination to satisfy
constraints with minimal cost.