A biased answer, based on Auroux's work http://arxiv.org/abs/1003.2962.

Auroux makes a connection between bordered Floer theory and an alternative approach, due to Lekili and myself, which is (still) under development, but which should include the $\pm$ and $\infty$ versions. We do have a preliminary paper out: http://arxiv.org/abs/1102.3160.

**A general set-up:** Say you have a compact symplectic manifold $(X,\omega_X)$; and a codim 2 symplectic submanifold $D$, whose complement $M$ is exact: ${\omega_X}|_M=d\theta$, say.

Key example: $X=Sym^g(F)$, where $F$ is a compact surface of genus $g$, and $\omega_X$ a suitable Kaehler form; $M=Sym^g(F-z)$, where $z\in F$.

**Forms of Floer cohomology**: There are various forms of Floer cohomology one can consider.

(i) As in $\widehat{HF}$ Heegaard theory, one can consider $HF^\ast_M(L_0,L_1)$, the Floer cohomology in $M$ of a pair of (exact) compact Lagrangian submanifolds of $M$. When $L_0$ and $L_1$ are spin, this can be defined as a $\mathbb{Z}$-module.

(ii) As in $HF^-$ Heegaard theory, one can consider the filtered Floer cohomology $HF^\ast_{X,D}(L_0,L_1)$ of a pair of compact Lagrangians $L_i\subset M$ as before. The coefficients are in $\mathbb{Z}[[U]]$. The differential counts holomorphic bigons in $X$, weighted by $U^n$ where $n$ is intersection number with $D$.

(iii) One can consider non-compact Lagrangians $L_i\subset M$ which go to infinity nicely (following the Liouville flow). These have *wrapped* Floer cohomology $HW^\ast(L_0,L_1)$, as well as "partially wrapped" variants. Wrapping concerns how one chooses to perturb $L_0$ at infinity. This version takes place in $M$, and (AFAIK) can't naturally be extended to something that takes place in $X$.

**Invariants for 3-manifolds with boundary.** A basic idea is that a 3-manifold $Y$ bounding $F$ should define a (generalized) Lagrangian submanifold $L_Y$ where $X=Sym^{g(F)}F$, as in the "key example" above. The collection of filtered Floer modules $HF^*_{X,D}(\Lambda, L_Y)$ as $\Lambda$ ranges over Lagrangian submanifolds of $M$ (more precisely, the module, over the compact filtered Fukaya category of $(X,D)$, defined by $L_Y$) should be an invariant of $Y$.

If one is interested only in the simpler groups $HF^*_M(\Lambda,L_Y)$, one can (in principle) determine these by looking at the finite collection of (partially wrapped) groups $HW^*(W_i,L_Y)$, where $W_i$ ranges over the thimbles for a certain Lefschetz fibration $M\to \mathbb{C}$. That is, one thinks of $L_Y$ as defining a module over the algebra $A_{LOT}$ formed by the sum of groups $HW^*(W_i,W_j)$. This follows from a deep theorem of Seidel about generating Fukaya categories by thimbles, adapted by Auroux.

The algebra $A_{LOT}$ is (part of) what Lipshitz-Ozsvath-Thurston assign to a parametrized surface, and the module is what they call $\widehat{CFA}(Y)$. They arrived at it by a quite different route. They don't bother with constructing $L_Y$ itself, only the module it defines. Because they use the groups of type (iii) to form their algebra, their approach only works in $M$, not $X$. For that reason, they only capture the hat-theory.

The great advantage of LOT's approach is its finiteness and computability. Lekili and I do construct $L_Y$. We can guess at finite collections of "test Lagrangians" sufficient to compute the module $HF^*_{X,D}(\cdot, L_Y)$, but have not yet proved that they are sufficient.